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Results for “DNA self-assembly”

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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119 records · Page 7
All sourcesNASA NTRSDOE OSTI
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↗
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

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 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 OSTI2024

Hopping and crawling DNA-coated colloids

Understanding the motion of particles with multivalent ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or roll, depending on the study. We shed light on this problem by observing DNA-coated colloids diffusing near surfaces coated with complementary strands for a wide array of coating designs. We find colloids rapidly switch between 2 modes: They hop—with long and fast steps—and crawl—with short and slow steps. Both modes occur at all temperatures around the melting point and over various designs. The particles become increasingly subdiffusive as temperature decreases, in line with subsequent velocity steps becoming increasingly anticorrelated, corresponding to switchbacks in the trajectories. Overall, crawling (or hopping) phases are more predominant at low (or high) temperatures; crawling is also more efficient at low temperatures than hopping to cover large distances. We rationalize this behavior within a simple model: At lower temperatures, the number of bound strands increases, and detachment of all bonds is unlikely, hence, hopping is prevented and crawling favored. We thus reveal the mechanism behind a common design rule relying on increased strand density for long-range self-assembly: Dense strands on surfaces are required to enable crawling, possibly facilitating particle rearrangements.

Science & Technology - Other Topics↗
DOE OSTI2019

Multivalent Cation-Induced Actuation of DNA-Mediated Colloidal Superlattices

Nanoparticles functionalized with DNA can assemble into ordered superlattices with defined crystal habits through programmable DNA “bonds”. Here, we examine the interactions of multivalent cations with these DNA bonds as a chemical approach for actuating colloidal superlattices. Multivalent cations alter DNA structure on the molecular scale, enabling the DNA “bond length” to be reversibly altered between 17 and 3 nm, ultimately leading to changes in the overall dimensions of the micrometer-sized superlattice. The identity, charge, and concentration of the cations each control the extent of actuation, with Ni2+ capable of inducing a remarkable >65% reversible change in crystal volume. In addition, these cations can increase “bond strength”, as evidenced by superlattice thermal stability enhancements of >60 °C relative to systems without multivalent cations. Molecular dynamics simulations provide insight into the conformational changes in DNA structure as the bond length approaches 3 nm and show that cations that screen the negative charge on the DNA backbone more effectively cause greater crystal contraction. Finally, taken together, the use of multivalent cations represents a powerful strategy to alter superlattice structure and stability, which can impact diverse applications through dynamic control of material properties, including the optical, magnetic, and mechanical properties.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2022

Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks

Engineered far-from-equilibrium synthetic chemical networks that pulse or switch states in response to environmental signals could precisely regulate the kinetics of chemical synthesis or self-assembly. Currently, such networks must be extensively tuned to compensate for the different activities of and unintended reactions between a network’s various chemical components. Modular elements with standardized performance could be used to rapidly construct networks with designed functions. Here we develop standardized excitable chemical regulatory elements, termed genelets, and use them to construct complex in vitro transcriptional networks. We develop a protocol for identifying >15 interchangeable genelet elements with uniform performance and minimal crosstalk. Furthermore, these elements can be combined to engineer feedforward and feedback modules whose dynamics match those predicted by a simple kinetic model. Modules can then be rationally integrated and organized into networks that produce tunable temporal pulses and act as multistate switchable memories. Standardized genelet elements, and the workflow to identify more, should make engineering complex far-from-equilibrium chemical dynamics routine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Mechanism of DNA origami folding elucidated by mesoscopic simulations

Abstract Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Mutations in artificial self-replicating tiles: A step toward Darwinian evolution

Significance In nature, mutation is the first step of evolution, where it provides the genetic variation for the natural selection to act. Here we take a system of artificial self-replicating tiles, DNA origami, that exhibit templated reproduction. We can generate a small fraction of mutations by introducing a mismatch in hybridization between parent and daughter. We can modify the origami functionality to affect the growth rate of the mutated species, giving it less or more evolutionary advantage, and to become dominant in several generations. The introduction of mutations into an artificial self-replicating system provides new directions for research into self-assembly processes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗