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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

SynopFrame: Multiscale time-dependent visual abstraction framework for analyzing DNA nanotechnology simulations

We present an open-source framework, SynopFrame, that allows DNA nanotechnology (DNA-nano) experts to analyze and understand molecular dynamics simulation trajectories of their designs. We use a multiscale multi-dimensional abstraction space, connect the representations to a projected conformational space plot of the structure’s temporal sequence, and thus enable experts to analyze the dynamics of their structural designs and, specifically, failure cases of the assembly. In addition, our time-dependent abstraction representation allows the biologists, for the first time in a smooth and structurally clear way, to identify and observe temporal transitions of a DNA-nano design from one configuration to another, and to highlight important periods of the simulation for further analysis. We realize SynopFrame as a dashboard of the different synchronized 3D spatial and 2D schematic visual representations, with a color overlay to show essential properties such as the status of hydrogen bonds. The linking of the spatial, schematic, and abstract views ensures that users can effectively analyze the high-frequency motion. We also categorize the status of the hydrogen bonds into a new format to allow us to color-encode it and overlay it on the representations. To demonstrate the utility of SynopFrame, we describe example usage scenarios and report user feedback.

Abstraction space↗
DOE OSTI2024

Six-Letter DNA Nanotechnology: Incorporation of Z-P Base Pairs into Self-Assembling 3D Crystals

Artificially expanded genetic information systems (AEGIS) were developed to expand the diversity and functionality of biological systems. Recent experiments have shown that these expanded DNA molecular systems are robust platforms for information storage and retrieval as well as useful for basic biotechnologies. In tandem, nucleic acid nanotechnology has seen the use of information-based “semantomorphic” encoding to drive the self-assembly of a vast array of supramolecular devices. To establish the effectiveness of AEGIS toward nanotechnological applications, we investigated the ability of a six-letter alphabet composed of A:T, G:C and synthetic Z:P (Z, 6-amino-3-(1'-β- D-2'-deoxy ribofuranosyl)-5-nitro-(1H)-pyridin-2-one; P, 2-amino-8-(1'- β-D-2'-deoxyribofuranosyl)-imidazo-[1,2a]-1,3,5-triazin-(8H)-4-one) base pairs to engage in 3D self-assembly. We found that crystals could be programmably assembled from AEGIS oligomers. We conclude that unnatural base pairs can be used for the topological self-assembly of crystals. We anticipate the expansion of AEGISbased nucleic acid nanotechnologies to enable the development of novel nanomaterials, high-fidelity signal cascades, and dynamic nanoscale devices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Control and synchronization of rapid nanoscale DNA heat engine by local heating

To further activate devices based on DNA nanotechnology, we introduce an approach that notably enhances both the speed and force of DNA powered machines and artificial hinge machine. A microheater, with millisecond response, heats or recools DNA origami constructs, hybridizing or dehybridizing sticky ends. Because anything within 20 micrometers of the heater equilibrates to a programmed temperature change in milliseconds, sticky ends of a compound DNA origami machine can open and close synchronously and operate cooperatively, in phase, additively increasing the drive force compared to single pair of sticky ends DNA machine (the six-helix bundle DNA origami hinge machine). In our demonstrations, we fold and unfold two square origami with 10 pairs of complementary sticky ends to drive a bead on the end of a rod like origami to speeds exceeding 30 micrometers per second. Our device envisions the creation of complex, synchronized DNA machines.

Science & Technology - Other Topics↗
DOE OSTI2026

DNA Crystals as a Template for Patterned Functional Materials

DNA nanotechnology offers a wide toolkit of molecular functionalities and scales, including intricate motifs less than 10 nm and periodic structures exceeding 100 µm. At larger scales, however, there are often significant tradeoffs for DNA structures, namely stability and mechanical strength. This work describes the design, synthesis, and characterization of a functionalized DNA crystal. Using a ligated DNA crystal grants significant freedom for various functional materials to be applied, in this case, semiconducting cadmium sulfide and palladium metal. Properties investigated in this study include stability, mechanical strength, and optoelectronic properties such as photoluminescence (PL) and electric conductivity. Significant changes are observed based on the functional material applied to DNA crystals. The Young's modulus of the crystal varies by about five orders of magnitude when functionalized with palladium. PL and semiconductive behaviors were observed when cadmium sulfide was attached. These crystals represent an expansion of the capabilities of DNA structures at these length scales, and additionally a platform for future studies exchanging the materials or altering the ligation scheme.

CdS↗
NASA NTRS2017

BioWires: Conductive DNA Nanowires in a Computationally-Optimized, Synthetic Biological Platform for Nanoelectronic Fabrication

DNA is an ideal template for a biological nanowire-it has a linear structure several atoms thick; it possesses addressable nucleobase geometry that can be precisely defined; and it is massively scalable into branched networks. Until now, the drawback of DNA as a conducting nanowire been, simply put, its low conductance. To address this deficiency, we extensively characterize a chemical variant of canonical DNA that exploits the affinity of natural cytosine bases for silver ions. We successfully construct chains of single silver ions inside double-stranded DNA, confirm the basic dC-Ag+-dC bond geometry and kinetics, and show length-tunability dependent on mismatch distribution, ion availability and enzyme activity. An analysis of the absorbance spectra of natural DNA and silver-binding, poly-cytosine DNA demonstrates the heightened thermostability of the ion chain and its resistance to aqueous stresses such as precipitation, dialysis and forced reduction. These chemically critical traits lend themselves to an increase in electrical conductivity of over an order of magnitude for 11-base silver-paired duplexes over natural strands when assayed by STM break junction. We further construct and implement a genetic pathway in the E. coli bacterium for the biosynthesis of highly ionizable DNA sequences. Toward future circuits, we construct a model of transcription network architectures to determine the most efficient and robust connectivity for cell-based fabrication, and we perform sequence optimization with a genetic algorithm to identify oligonucleotides robust to changes in the base-pairing energy landscape. We propose that this system will serve as a synthetic biological fabrication platform for more complex DNA nanotechnology and nanoelectronics with applications to deep space and low resource environments.

DNA↗
DOE OSTI2025

Energy Exchange in Dynamic DNA-Metal Hybrid Materials (Final Technical Report)

This report details research results from the 1 year renewal of DE-SC0017270, Energy Exchange in Dynamic DNA-Metal Hybrid Materials, including the primary findings associated with this research. This work investigated interactions between dynamic DNA origami energy harvesting materials and inorganic materials responsive to electromagnetic fields with two primary areas of inquiry: cyclic energy conversion and mechanical energy storage and transfer. This work resulted in 5 publications, including 1 in revision, and 1 issued patent.

36 MATERIALS SCIENCE↗
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 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 OSTI2025

Nanotubes Growth by Self-Assembly of DNA Strands at Room Temperature

Artificial biomolecular nanotubes are a promising approach to building materials mimicking the capacity of the cellular cytoskeleton to grow and self-organize dynamically. Nucleic acid nanotechnology has demonstrated a variety of self-assembling nanotubes with programmable, robust features and morphological similarities to actual cytoskeleton components. However, their production typically requires thermal annealing, which not only poses a general constraint on their potential applications but is also incompatible with physiological conditions. Here, we demonstrate that DNA nanotubes can self-assemble from a simple mixture of five short DNA strands at constant room temperature, growing for extended periods of time in bulk conditions as well as under confinement. Assembly is achieved using a monovalent salt buffer, which ensures a faithful nanoscale arrangement and avoids nanotube aggregation. We observe the formation of individual nanotubes up to 20 days with a diameter of 22 ± 4 nm and length of several tens of micrometers. We finally encapsulate the strands in microsized compartments, such as water-in-oil microdroplets and giant unilamellar vesicles serving as simple cell models. Notably, nanotubes not only isothermally self-assemble directly inside the microcompartments but also self-organize into dynamic higher-order structures resembling rings and dynamic networks. Our study provides an advantageous method for in situ assembly of programmable biomolecular scaffolds and materials using synthetic DNA strands without requirements of thermal treatment.

Chemistry↗
DOE OSTI2026

Effect of Thermodynamic and Environmental Factors on Crystallization of DNA‐Origami Superlattices

The directed self‐assembly of nanoscale materials into ordered superlattices presents a powerful strategy for creating next‐generation materials with programmable mechanical, optical, and photonic properties. Deoxyribonucleic acid (DNA) origami has emerged as a versatile scaffold for encoding nanoscale geometry and guiding the crystallization of complex 3D architectures. However, a systematic understanding of the parameters that govern the efficiency and quality of superlattice formation remains limited. In this study, we utilize octahedral DNA nanoscale frames as a model system to investigate the relative influence of key factors, including buffer composition, ionic strength, frame concentration, and thermal annealing protocols, on the size, order, and reproducibility of the resulting superlattices. Our findings provide a quantitative framework to rationally optimize DNA‐based assembly pathways. Structural characterization via small‐angle x‐ray scattering (SAXS), scanning electron microscopy (SEM), and optical microscopy validates the quality and fidelity of the assembled lattices. Moreover, by templating these DNA frameworks into inorganic replicas, we establish general design principles that extend beyond biomolecular systems, providing a foundation for the synthesis of programmable materials in broader nanofabrication contexts.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

DNA Origami Incorporated into Solid-State Nanopores Enables Enhanced Sensitivity for Precise Analysis of Protein Translocations

The rapidly advancing field of nanotechnology is driving the development of precise sensing methods at the nanoscale, with solid-state nanopores emerging as promising tools for biomolecular sensing. Here, this study investigates the increased sensitivity of solid-state nanopores achieved by integrating DNA origami structures, leading to the improved analysis of protein translocations. Using holo human serum transferrin (holo-hSTf) as a model protein, we compared hybrid nanopores incorporating DNA origami with open solid-state nanopores. Results show a significant enhancement in holo-hSTf detection sensitivity with DNA origami integration, suggesting a unique role of DNA interactions beyond confinement. This approach holds potential for ultrasensitive protein detection in biosensing applications, offering advancements in biomedical research and diagnostic tool development for diseases with low-abundance protein biomarkers. Further exploration of origami designs and nanopore configurations promises even greater sensitivity and versatility in the detection of a wider range of proteins, paving the way for advanced biosensing technologies.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

Directing Assembly of Mesoscale Multi‐Shell Morphologies of DNA Origami Crystals

Nature builds hierarchically ordered materials, such as seashells, wood, and bones, through spatially and temporally regulated growth. Mimicking such a level of control in synthetic systems remains challenging, particularly in achieving multiscale organizations with prescribed nanoscale arrangements and desired material morphologies. In this study, we introduce a DNA-based self-assembly strategy for constructing diverse multi-shell mesoscale morphologies from nanoscale lattices, enabling prescribed structural, and compositional 3D material patterns. Using DNA origami frames as modular monomers, we direct anisotropic epitaxial growth through addressable DNA frame binding motifs and encapsulate nanoparticles (NPs) in desired 3D patterns. Sequential monomer addition under thermodynamically favorable conditions enables shell growth through heterogeneous nucleation while minimizing unwanted homogeneous nucleation. Here, we demonstrate that DNA-encoded addressability enables epitaxial shell growth along specific lattice directions, yielding crystals with multilayered mesoscale organization, including tube-like (sushi roll) and plate-like (macaron) morphologies. Shell-specific NP configurations and compositions are achieved through addressable and differentiated placement of NPs within each shell, as validated by small-angle x-ray scattering and cross-sectional scanning transmission electron microscopy. We further demonstrate addressable NP release and reveal that shells modulate release kinetics. Together, these findings establish a platform for fabricating DNA origami crystals with programmable mesoscale morphologies, nanoscale structure, composition, and transport properties.

3D patterning↗
DOE OSTI2026

Structural and compositional complexities of hierarchical self-assembly: A hypergraph approach

Programmable self-assembly enables the construction of complex molecular, supramolecular, and crystalline architectures from well-designed building blocks. In this work, we introduce a hypergraph-based formalism, Blocks & Bonds (B&B), which generalizes classical chemical graph theory by incorporating directed and multicolored interactions, internal symmetries, and hierarchical organization. Within this framework, we develop the Structure Code (SC), a compact and versatile language for describing self-assembled architectures. We define a Kolmogorov-style structural complexity as the total information content of SC, obtained through its tokenization and Shannon information assignment. Complementing this encoding-based measure, we introduce a much simpler quantity, the compositional complexity, which depends only on the number and cumulative usage of block and bond types in the construction set. A central result of this work is a strong empirical correlation between the token-based structural complexity and the compositional complexity across all examined systems. Owing to this agreement, the compositional complexity emerges as the most practical and broadly applicable measure: it is easy to compute, requires no explicit encoding, and yet closely tracks the actual information content of structurally diverse architectures. Applications to molecular systems (ethylene glycol and glucose), DNA-origami lattices, and crystalline assemblies show that B&B hypergraphs provide a unified, scalable, and information-efficient representation of structural organization, naturally capturing symmetry, modularity, and stereochemistry. This framework establishes a quantitative foundation for complexity-aware classification and inverse design of programmable matter.

36 MATERIALS SCIENCE↗