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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

Understanding the structural mechanics of ligated DNA crystals via molecular dynamics simulation

DNA self-assembly is a highly programmable method to construct arbitrary architectures based on sequence complementarity. Among various constructs, DNA crystals are macroscopic crystalline materials formed by assembling motifs via sticky end association. Due to their high structural integrity and size ranging from tens to hundreds of micrometers, DNA crystals offer unique opportunities to study the structural properties and deformation behaviors of DNA assemblies. For example, enzymatic ligation of sticky ends can selectively seal nicks resulting in more robust structures with enhanced mechanical properties. However, the research efforts have been mostly on experiments involving different motif designs, structural optimization, or new synthesis methods, while their mechanics are not yet fully understood. The complex properties of DNA crystals are difficult to study via experiments alone, and numerical simulation can complement and aid the experiments. The coarse-grained molecular dynamics (MD) simulation is a powerful tool that can probe the mechanics of DNA assemblies. Here, we investigate DNA crystals made of four different motif lengths with various ligation patterns (full ligation, major directions, connectors, and in-plane) using oxDNA, an open-source, coarse-grained MD platform. We found that several distinct deformation stages emerge in response to mechanical loading and that the number and the location of ligated nucleotides can significantly modulate structural behaviors. These findings should be useful for predicting crystal properties and thus improving the design.

DNA crystal↗
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 NTRS1996

Mobility of Electron in DNA Crystals by Laser Radiation

The mobility of electrons in laser radiated DNA is closed to the energy transfer and energy migration of a biological molecule. Arrhenius has studied the conductivity of the electrons in a biological molecule. But his result is far from the experimental result and meanwhile the relation between some parameters in his theory and the micro-quantities in DNA is not very clear. In this paper, we propose a new phonon model of electron mobility in DNA and use Lippman-Schwinger equation and S-matrix theory to study the mobility of electrons in DNA crystal. The result is relatively close to the experiment result and some parameters in Arrhenius theory are explained in our work.

Zhang, Kaixi↗
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 OSTI2025

Organic Modulators Enable Morphological Diversity in Colloidal Crystals Engineered with DNA

Colloidal crystal engineering with DNA is a powerful way of generating a wide variety of crystals spanning over 90 different symmetries. However, in many cases, crystals with well-defined habits are difficult, if not impossible, to make, in part due to rapid crystal defect formation and propagation. This is especially true in the case of face-centered cubic (FCC) structures. Herein, we report a strategy that uses formamide as a chemical modulator to slow down colloidal crystal growth, which decreases defect formation and yields higher-quality crystals. Formamide forms hydrogen bonds with DNA bases and destabilizes the DNA duplex; in the context of colloidal crystallization, formamide leads to the disassembly of undercoordinated particles (defect architectures) and facilitates their reassembly into structures with the maximum number of nearest-neighbor contacts and DNA bonds. Here, when targeting an FCC lattice comprised of DNA-modified spherical 20 nm particles, formamide promotes the formation of its Wulff polyhedron (a truncated octahedron), never observed before in colloidal crystal engineering with DNA. Importantly, kinetic habits, including tetrahedra, octahedra, icosahedra, and decahedra, are also observed depending on formamide concentration.

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

Revealing and Engineering Assembly Pathways of 3D DNA Origami Crystals

Recent developments in nanomaterial self-assembly demonstrate the capability to create tailored nanostructures by engineering both the binding coordination and specificity of interactions between material subunits. DNA origami frames allow for the design and fabrication of a broad variety of ordered 3D nanoscale architectures through self-assembly, facilitated by frame-to-frame bonds with designable strength and specificity. While the bond design is critical to lattice formation, the assembly process itself is often dependent on a thermal pathway. Highly ordered nanoscale frameworks, assembled from DNA frames, are predominantly crystallized through thermal annealing pathways that typically follow a “slow” cooling approach, with experiments on the time scale of days yielding DNA origami crystals in the range of 1−10 μm. This extended assembly time scale hinders the study of crystal formation pathways, necessitating a deeper understanding of factors governing successful annealing. Lack of insight into time scale also presents a practical limitation for material fabrication. Here, we investigate key factors affecting lattice assembly pathways and demonstrate that precise engineering of assembly conditions greatly reduces assembly times by up to nearly 2 orders of magnitude. We evaluate the nucleation and growth of crystals via optical and electron microscopy, and small-angle X-ray scattering techniques, mapping the time−temperature-transformation of superlattices from the melt through single-crystal optical tracking. The results show that origami frame assembly can be described by classical nucleation and growth theory, which can, in turn, be used to prescribe the growth of the crystals. Lastly, these findings are applied to demonstrate thermal pathway-dependent assembly, forming distinct assemblies based on different thermal annealing profiles.

36 MATERIALS SCIENCE↗
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

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 OSTI2026

Diffraction-quality, ultraflexible protein single crystals engineered with DNA

DNA-functionalized colloidal nanoparticles assemble through flexible, nanoscale DNA hybridization interactions that limit atomic-level structural order. Here, we report a valence-centric strategy that enables DNA-bonded, protein single crystals with unconventional mechanical properties. An octameric enzyme, glutarate L-2-hydroxylase, was site- and number-selectively conjugated with eight self-complementary single-stranded DNA, yielding octavalent molecular bonds. The resulting conjugate assembled into the designed body-centered tetragonal crystals that diffracted to 1.42- to 2.61-angstrom resolution, with contacts mediated by B-form DNA helices spanning 17 to 25 angstroms. Increasing oligonucleotide length induces anisotropic lattice expansion while preserving atomic periodicity, even with partial DNA occupancy. Mechanistic studies suggest that the dynamic motion of unhybridized DNA facilitates crystallization, analogous to fluctuating electron clouds in atomic bonding. Compared with native protein crystals, DNA-hybridized crystals are 23-fold softer. These results challenge the assumption that flexibility is incompatible with structural order and establish a programmable framework for biomolecular crystallization and nanomaterials engineering with atomic precision.

Han, Zhenyu [Department of Chemistry, Northwestern↗
DOE OSTI2024

High Temperature, Isothermal Growth Promotes Close Packing and Thermal Stability in DNA-Engineered Colloidal Crystals

Here, we report a strategy to accelerate the synthesis and increase the crystallinity of colloidal crystals engineered with DNA. Specifically, by holding the DNA-modified Au particle building blocks above the T m of the individual nanoparticle building blocks, but slightly below the T m of the anticipated colloidal crystal during the assembly process, crystallinity is increased, and enthalpically-favored phases with high degrees of facet registration are observed. We studied the utility of this approach with systems for which the commonly adopted slow-cooling approach yielded primarily amorphous aggregates. In particular, we used it to synthesize high-volume fraction colloidal crystals from large (80 nm) anisotropic nanoparticles (cubes and rhombic dodecahedra) with short (<14 nm) DNA designed to restrict the degrees of freedom for the DNA bonds and maintain the anisotropy of the particle building block. Small-angle X-ray scattering and electron microscopy studies show that the crystalline phases synthesized via this method are more thermally stable than their corresponding aggregate phases, likely due to an increased number of DNA-DNA bonds between particles. Crystal size tunability (between 0.5 and 15 µm edge lengths) and epitaxial growth were demonstrated using this strategy by modulating the NaCl concentration in tandem with previously synthesized colloidal crystal nuclei. Taken together, this isothermal strategy provides a route to deliberately crystallize a wide variety of anisotropic colloidal materials and expands the phase space accessible to nanoparticles modified with DNA.

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

Symmetry-Breaking Dendrimer Synthons in Colloidal Crystal Engineering with DNA

Breaking symmetry in colloidal crystals is challenging due to the inherent chemical and structural isotropy of many nanoscale building blocks. If a non-particle component could be used to anisotropically encode such building blocks with orthogonal recognition properties, one could expand the scope of structural and compositional possibilities of colloidal crystals beyond what is thus far possible with purely particle-based systems. In this work, we report the synthesis and characterization of novel DNA dendrimers that function as symmetry-breaking synthons, capable of programming anisotropic and orthogonal interactions within colloidal crystals. When the DNA dendrimers have identical sticky ends, they hybridize with DNA-functionalized nanoparticles to yield three distinct colloidal crystals, dictated by dendrimer size, including a structure not previously reported in the field of colloidal crystal engineering, Si 2 Sr. When used as symmetry-breaking synthons (when the sticky ends deliberately consist of orthogonal sequences), the synthesis of binary and ternary colloidal alloys with structures that can only be realized through directional interactions is possible. Furthermore, by modulating the extent of shape anisotropy within the DNA dendrimers, the local distribution of the nanoparticles within the crystals can be directed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗