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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

DNA Strand Displacement Driven Molecular Additive Manufacturing (DSD-MAM)

The goal of this project was to validate two-dimensional molecular printers, initially selfassembled from DNA and then actuated by externally driven cycles of DNA strand displacement, as prototype integrated nanosystems for molecular additive manufacturing. Novel functionalities of these nanomachines were explored during this project, including the following: nanometer-precision positioning mechanisms based on DNA strand displacement with multivalent interactions for discrete stepping or else diffusive capture; integration of independently moving layers of DNA origami to achieve 2D controllable motion; integration of spatial positioning with deposition functionality. The principal importance of this project was to provide an essential step in the development of a new technology for atomically precise manufacturing. Our first generation molecular 2D printer offers several advantages over conventional DNA-origami patterning, such as faster prototyping, faster dynamic rearrangement of patterns, and the ability to respond with feedback. We anticipate that our first-generation molecular printers may inspire future generations of molecular printers with iterative improvements in robustness and throughput. Potential applications of atomically precise manufacturing include the following: photovoltaics; photosynthetic and fuel cells; thermoelectrics and anisotropic heat spreaders; solid-state lighting; molecular electronic and plasmonic circuits; selectively preamble membranes; self-repairing materials with high strength-to-weight and fracture resistance.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Binding kinetics of harmonically confined random walkers

Diffusion-mediated binding of molecules under the influence of discrete spatially confining potentials is a commonly encountered scenario in systems subjected to explicit fields or implicit fields arising from tethering restraints. Here, in this work, we derive analytical expressions for the mean binding time of two random walkers geometrically confined by means of two harmonic potentials in one- and two-dimensional systems, which show excellent agreement with Brownian dynamics simulations. As a demonstration of its utility, we use this theory to maximize the communication speed in existing DNA walkers, obtaining quantitative agreement with previously reported experimental findings. The analytical expressions derived in this paper are broadly applicable to diverse systems, providing ways to characterize communication processes and optimize the rate of signal propagation for sensing and computing applications at the nanoscale.

36 MATERIALS SCIENCE↗
DOE OSTI2025

An Innovative High Throughput Genome Releaser for Rapid and Efficient PCR Screening

High-throughput PCR screening is vital in synthetic biology and metabolic engineering as it allows researchers to rapidly analyze and detect numerous targeted genetic mutation in the genome. Current challenges for high-throughput PCR screening in synthetic biology include efficiently preparing genomic DNA, optimizing protocols for diverse sample types, managing contamination risks, and effectively analyzing the large volumes of data generated while ensuring consistent and accurate results. In this study, we present the development of a High Throughput Genome Releaser (HTGR), an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed based on a squash method for rapid, cost-effective, and efficient DNA release, optimized for subsequent PCR reactions. After experimenting with various synthetic materials, we selected a plastic that closely replicates the smooth surface and compression properties of microscope slides, ensuring reliable performance. We engineered a device featuring a 96-Well Plate and a shear applicator, operable both manually and automatically, and compatible with standard liquid-handling robot platform. This compatibility enhances ease of use in high-throughput PCR workflows. Additionally, we developed software to support its automatic functions. Our results demonstrated that the specially engineered 96-Well Plate and HTGR can effectively squash fungal spores , which release enough genome DNA for PCR screening. The genome releaser facilitates the preparation of PCR-amplifiable genomic DNA substrate from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells, which could significantly advance biomanufacturing processes.

Yuan, Guoliang [BATTELLE (PACIFIC NW LAB)]↗
DOE OSTI2024

High Throughput Genome Releaser

In this study, we present the development of a High Throughput Genome Releaser, an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed for rapid, cost-effective, and efficient DNA extraction, optimized for subsequent PCR reactions. Our experimentation with various synthetic materials led us to select a particular type of plastic that mirrors the properties of glass cover slides, providing a smooth surface and effective compression capabilities. We engineered a 96-well device equipped with a 96-well plate and a top rod, operable both manually and automatically, which is compatible with widely used liquid-handling robot decks. This compatibility enhances ease of use in high-throughput PCR setups. Additionally, we developed software to support its automatic functions. The genome releaser facilitates the extraction of PCR-amplifiable genomic DNA from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells. This versatility could significantly advance biomanufacturing processes.

42 ENGINEERING↗
DOE OSTI2023

Regulating phase behavior of nanoparticle assemblies through engineering of DNA-mediated isotropic interactions

Self-assembly of isotropically interacting particles into desired crystal structures could allow for creating designed functional materials via simple synthetic means. However, the ability to use isotropic particles to assemble different crystal types remains challenging, especially for generating low-coordinated crystal structures. Here, we demonstrate that isotropic pairwise interparticle interactions can be rationally tuned through the design of DNA shells in a range that allows transition from common, high-coordinated FCC-CuAu and BCC-CsCl lattices, to more exotic symmetries for spherical particles such as the SC-NaCl lattice and to low-coordinated crystal structures (i.e., cubic diamond, open honeycomb). The combination of computational and experimental approaches reveals such a design strategy using DNA-functionalized nanoparticles and successfully demonstrates the realization of BCC-CsCl, SC-NaCl, and a weakly ordered cubic diamond phase. The study reveals the phase behavior of isotropic nanoparticles for DNA–shell tunable interaction, which, due to the ease of synthesis is promising for the practical realization of non-close-packed lattices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Formation and surface melting of nanoparticle superlattices in a solution

The wisdom in the saying of “There are no two snowflakes alike” lies in the importance of history or kinetic pathways in the phase transitions of solids. Likewise, “artificial solids,” namely superlattices consisting of functional nanoparticles, have lattice size, surface morphology, crystallinity, symmetry, and structural reconfiguration (for example, transition into a disordered state) highly dependent on the kinetic pathways as the nanoparticles interact with each other in solution [1]. Great progresses have been made in understanding the formation pathways of superlattices using liquid-phase transmission electron microscopy (TEM) [2-4]. For example, by tracking single nanoparticle’s trajectories, especially aided by U-net neural network-based machine learning, previous studies mapped the fundamental nanoparticle interactions at nanometer resolution [5]. Nonclassical, two-step nucleation pathway has also been elucidated in the system of nanoprisms, by optimizing protocols such as loading nanoparticle suspensions over the supersaturation threshold and minimizing particle‒substrate interaction [2]. Surface morphologies or exposed facets of superlattices have been shown to follow the principles of Wulff construction rule, where the facet-dependent surface energy can be measured based on the capillary wave theory [4]. However, the reverse process of crystallization of superlattices, the conversion from crystalline to disordered state, has been much less explored. On one hand, the melting of nanoparticle superlattices can provide a preferred pathway to induce structural reorganization or shuffling of building blocks for them to transform into different types of crystal structures. On the other hand, understanding nanoscale superlattice melting and comparing such behaviors with the prevailing surface melting theories developed for atomic/molecular solids can provide a potent way to engineer phase transitions of supra- and hierarchical structures constructed from nanoscale entities (e.g., DNA-coated nanoparticles, proteins), for their applications in reprogrammable and switchable materials with multifunctional properties [6, 7]. The experimental challenges to observe melting of superlattices are twofold. Practically it is difficult to load the initial superlattice form, in an intact manner, into the highly confined liquid-phase TEM chamber for in-situ observation. Here, the triggering of melting also needs meticulous manipulation of nanoparticle concentration, interparticle interaction, and solution environment.

Kim, Ahyoung↗
DOE OSTI2025

Light-Modulated Self-Assembly of Synthetic Nanotubes

Artificial biomolecular polymers with the capacity to respond to stimuli are emerging as a key component to the development of living materials and synthetic cells. Here, in this work, we demonstrate artificial DNA tubular nanostructures that form in response to light in a dose-dependent manner. These nanotubes assemble from programmable DNA tile motifs that are engineered to include a UV-responsive domain so that UV irradiation activates nanotube self-assembly. We demonstrate that the nanotube formation speed can be tuned by adjusting the UV dose. We then couple the light-dependent activation of tiles with RNA transcription, making it possible to control nanotube formation via concurrent physical and biochemical stimuli. Finally, we illustrate how UV activation effectively controls nanotube assembly in confinement as a rudimentary stimulus-responsive cytoskeletal system that can achieve various conformations in a minimal synthetic cell. This study contributes new tile designs that are immediately useful to building biomolecular scaffolds with controllable dynamics in response to multiple stimuli.

DNA nanotechnology↗
DOE OSTI2025

Volumetric Shaping of Nanoparticle-DNA Crystals by Light-Induced Milling

DNA-programmable self-assembly enables the formation of nanoparticle crystals with controlled lattice symmetry. While this approach offers the formation of complexly ordered nanostructures for optical, mechanical, and biological applications, a mesoscale control over such nanomaterials is limited. Directing the material formation process through the assembly pathway or external fields allows for modulating crystal morphology, but achieving arbitrary morphology remains challenging. Here, we present a photothermal method for shaping 3D DNA-programmable crystals of gold nanoparticles. Through local heating of nanoparticles due to plasmonic light absorption, we induce targeted volumetric dissolution of specifically defined crystal areas with micron-scale accuracy. This technique effectively prescribes crystal shaping and creates arbitrarily shaped voids within crystals. We further investigate both computationally and experimentally the key factors governing volumetric material subtraction. The developed automated light-milling platform enables the fabrication of nanomaterials exhibiting both DNA-programmable nanoscale order and custom-designed mesoscale architecture.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Mix and match—a versatile equilibrium approach for hybrid colloidal synthesis

Colloidal synthesis is a powerful bottom-up approach for programmed self-assembly which holds promise for both research and industry. While diverse, each synthetic process is typically restricted to a specific chemistry. Many applications however require composite materials, whereas a chemical equilibrium can typically only match one material but not the other. Here, a scalable general approach is presented, alleviating the dependency on a specific chemical reaction, by resorting to a mechanical equilibrium; an isopycnic density-gradient-step is tailored to form clusters with prescribed composition. Valence control is demonstrated, making dimers, trimers, and tetramers with purity as high as 96%. The measured kinetics shows a scaleable throughput. The density gradient step plays a dual role of both filtering out undesired products and concentrating the target structures. The “Mix-and-Match” approach is general, and applies to a broad range of colloidal matter: diverse material compositions (plastics, glasses, and emulsions); a range of colloidal interactions (van der Waals, Coulomb, and DNA hybridization); and a spectrum of sizes (nanoscale to multiple micrometers). Lastly, the strength of the method is displayed by producing a monodisperse suspension from a highly polydisperse emulsion. The ability to combine colloids into architectures of hybrid materials has applications in pharmaceuticals, cosmetics, and photonics.

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

Harnessing Particle Size‐Control and DNA‐Oligo Functionalization in ZIF‐76 for Biological Applications

Abstract Advanced therapeutics require novel nanocarriers to ensure their functionality is preserved during transit. Zeolitic imidazolate frameworks (ZIFs) have emerged as promising materials in this field owing to their combined biocompatibility, high porosity, and tunable chemistry. While a diverse family of ZIFs has been reported, few have been explored beyond the prototypical ZIF‐8. Herein, the size‐controlled synthesis of three distinct ZIF‐76 analogs is demonstrated, overcoming the unique synthetic challenges intrinsic to the lta topology and complex crystallization kinetics associated with the mixed linker approach. This assesses the materials’ platform effectiveness for intracellular delivery first by exploring the structural and colloidal stability in biologically relevant media. To circumvent particle aggregation, fluorescently labeled DNA oligonucleotides are post‐synthetically attached to the ZIF surface. This modification significantly improves the colloidal stability in media and facilitates particle internalization tracking. Finally, the particle‐cell interactions are assessed, revealing rapid cell membrane association with macrophages, but not lung epithelial cells, and ZIF accumulation within macrophages which increased over time. Importantly, this study outlines a generalized approach toward expanding the available library of ZIFs for biological applications, enabling the potential for targeted therapeutic delivery for intracellular infections treatment.

Deneff, Jacob I.↗
DOE OSTI2022

Controlling morphology in hybrid isotropic/patchy particle assemblies

Brownian dynamics is used to study self-assembly in a hybrid system of isotropic particles (IPs), combined with anisotropic building blocks that represent special “designer particles.” Those are modeled as spherical patchy particles (PPs) with binding only allowed between their patches and IPs. In this study, two types of PPs are considered: Octahedral PPs (Oh-PPs) and Square PPs (Sq-PPs), with octahedral and square arrangements of patches, respectively. The self-assembly is additionally facilitated by the simulated annealing procedure. Here, the resultant structures are characterized by a combination of local correlations in cubatic ordering and a symmetry-specific variation of bond orientation order parameters (SymBOPs). By varying the PP/IP size ratio, we detected a sharp crossover between two distinct morphologies in both types of systems. High symmetry phases, NaCl crystal for Oh-PP and square lattice for Sq-PP, are observed for larger size ratios. For the smaller ones, the dominant morphologies are significantly different, e.g., Oh-PPs form a compact amorphous structure with predominantly face-to-face orientation of neighboring PPs. Unusually, for a morphology without a long-range order, it is still possible to identify well organized coherent clusters of this structure, thanks to the adoption of our SymBOP-based characterization.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Genomic reconstruction of Bacillus anthracis from complex environmental samples enables high-throughput identification and lineage assignment in Pakistan

Bacillus anthracis, the causative agent of anthrax, is a highly virulent zoonotic pathogen primarily affecting domesticated and wild herbivores. Human exposure to B. anthracis is primarily through contact with infected animals or contaminated animal products. In Pakistan, where livestock vaccines are largely unavailable and infected carcasses are often disposed of improperly, the risk to humans, wildlife and livestock is significant. Currently, the diagnosis of anthrax infections and outbreak tracing necessitates the isolation and culturing of B. anthracis, a process that requires BSL-3 facilities. In this study, we show that positive identification, genome reconstruction and lineage assignment can be accomplished using bioinformatic analysis of DNA extracted directly from environmental samples that would otherwise provide the starting material for isolation and culturing. This approach does not require laboratory target enrichment as is necessary for other pathogens, due in part to the extremely high bacterial load in the bloodstream in the deceased animals. Using these methods, we greatly expand the knowledge of endemic B. anthracis in Pakistan. We provide the first reference B. anthracis genomes from Pakistan since the 1970s and identify A.Br.014 Aust94 as a minor circulating sublineage alongside the dominant A.Br.047 Vollum. Future work will focus on the limits of detection and will determine if this bioinformatic method can be expanded more broadly for B. anthracis or other pathogens to replace typical culture-based methods.

A.Br.047 Vollum↗
DOE OSTI2022

Shape memory in self-adapting colloidal crystals

We report reconfigurable, mechanically responsive crystalline materials are central components in many sensing, soft robotic, and energy conversion and storage devices1,2,3,4. Crystalline materials can readily deform under various stimuli and the extent of recoverable deformation is highly dependent upon bond type1,2,5,6,7,8,9,10. Indeed, for structures held together via simple electrostatic interactions, minimal deformations are tolerated. By contrast, structures held together by molecular bonds can, in principle, sustain much larger deformations and more easily recover their original configurations. In this report we study the deformation properties of well-faceted colloidal crystals engineered with DNA. These crystals are large in size (greater than 100 µm) and have a body-centred cubic (bcc) structure with a high viscoelastic volume fraction (of more than 97%). Therefore, they can be compressed into irregular shapes with wrinkles and creases, and, notably, these deformed crystals, upon rehydration, assume their initial well-formed crystalline morphology and internal nanoscale order within seconds. For most crystals, such compression and deformation would lead to permanent, irreversible damage. The substantial structural changes to the colloidal crystals are accompanied by notable and reversible optical property changes. For example, whereas the original and structurally recovered crystals exhibit near-perfect (over 98%) broadband absorption in the ultraviolet–visible region, the deformed crystals exhibit significantly increased reflection (up to 50% of incident light at certain wavelengths), mainly because of increases in their refractive index and inhomogeneity.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Oblique Packing and Tunable Excitonic Coupling in DNA‐Templated Squaraine Rotaxane Dimer Aggregates

Abstract When molecules are aggregated such that their excited states form delocalized excitons, their spatial arrangement, or packing, can be coarsely controlled by templating and finely controlled by chemical substitution; however, challenges remain in controlling their packing on intermediate length scales. Here, we use an approach based on mechanically interlocked molecules to promote an elusive oblique packing arrangement in a series of three squaraine rotaxane dimers. We template the squaraine rotaxane dimers using DNA and observe two excitonically split bands of near‐equal intensity in their absorption spectra – a distinct signature of oblique packing, validated by theoretical modeling of the experimental results. Additional fine control of packing is demonstrated by fluorinating the macrocycle of the rotaxane, which promotes denser packing and stronger excitonic interactions.

36 MATERIALS SCIENCE↗
DOE OSTI2022

The nanocaterpillar's random walk: diffusion with ligand–receptor contacts

Particles with ligand–receptor contacts bind and unbind fluctuating “legs” to surfaces, whose fluctuations cause the particle to diffuse. Quantifying the diffusion of such “nanoscale caterpillars” is a challenge, since binding events often occur on very short time and length scales. Here, in this work, we derive an analytical formula, validated by simulations, for the long time translational diffusion coefficient of an overdamped nanocaterpillar, under a range of modeling assumptions. We demonstrate that the effective diffusion coefficient, which depends on the microscopic parameters governing the legs, can be orders of magnitude smaller than the background diffusion coefficient. Furthermore it varies rapidly with temperature, and reproduces the striking variations seen in existing data and our own measurements of the diffusion of DNA-coated colloids. Our model gives insight into the mechanism of motion, and allows us to ask: when does a nanocaterpillar prefer to move by sliding, where one leg is always linked to the surface, and when does it prefer to move by hopping, which requires all legs to unbind simultaneously? We compare a range of systems (viruses, molecular motors, white blood cells, protein cargos in the nuclear pore complex, bacteria such as Escherichia coli, and DNA-coated colloids) and present guidelines to control the mode of motion for materials design.

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

Planar 2D wireframe DNA origami

Two-dimensional (2D) DNA origami is widely used for applications ranging from excitonics to single-molecule biophysics. Conventional, single-layer 2D DNA origami exhibits flexibility and curvature in solution; however, that may limit its suitability as a 2D structural template. In contrast, 2D wireframe DNA origami rendered with six-helix bundle edges offers local control over duplex orientations with enhanced in-plane rigidity. Here, we investigate the 3D structure of these assemblies using cryo–electron microscopy (cryo-EM). 3D reconstructions reveal a high degree of planarity and homogeneity in solution for polygonal objects with and without internal mesh, enabling 10-Å resolution for a triangle. Coarse-grained simulations were in agreement with cryo-EM data, offering molecular structural insight into this class of 2D DNA origami. Our results suggest that these assemblies may be valuable for 2D material applications and geometries that require high structural fidelity together with local control over duplex orientations, rather than parallel duplex assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evolution of nanopores in hexagonal boron nitride

Abstract The engineering of atomically-precise nanopores in two-dimensional materials presents exciting opportunities for both fundamental science studies as well as applications in energy, DNA sequencing, and quantum information technologies. The exceptional chemical and thermal stability of hexagonal boron nitride (h-BN) suggest that exposed h-BN nanopores will retain their atomic structure even when subjected to extended periods of time in gas or liquid environments. Here we employ transmission electron microscopy to examine the time evolution of h-BN nanopores in vacuum and in air and find, even at room temperature, dramatic geometry changes due to atom motion and edge contamination adsorption, for timescales ranging from one hour to one week. The discovery of nanopore evolution contrasts with general expectations and has profound implications for nanopore applications of two-dimensional materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗