Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,495 records · Page 83
All sourcesNASA NTRSDOE OSTI
NASA NTRS2002

Nucleation and Growth According to Lysozyme

How does one take a molecule, strongly asymmetric in both shape and charge distribution, and assemble it into a crystal? We propose a model for the nucleation and crystal growth process for tetragonal lysozyme that may be very germane to other monomeric proteins. The first species formed is postulated to be a dimer. Through repeating associations involving the same intermolecular interactions this becomes the 4(sub 3) helix, that in turn serves as the basic unit for nucleation and crystal growth. High salt attenuates surface charges while promoting hydrophobic interactions. Symmetry facilitates helix self-association. Assembly stability is enhanced when a four helix structure is obtained, with each bound to two neighbors. Only two unique interactions are required. The first are those for helix formation, where the dominant interaction is the intermolecular bridging anion. The second is the anti-parallel side-by-side helix-helix interaction, guided by alternating pairs of symmetry related salt bridges along each side. At this stage all eight unique positions of the P4(sub 3)2(sub 1)2(sub 1) unit cell are filled. From the above, the process is one of a) attenuating the most strongly interacting groups, such that b) the molecules begin to self-associate in defined patterns, so that c) symmetry is obtained, which d) propagates as a growing crystal. Simple and conceptually obvious in hindsight, this tells much about what we are empirically doing when we crystallize macromolecules. By adjusting the solution parameters we are empirically balancing the intermolecular interactions, preferentially attenuating the dominant strong (for lysozyme the charged groups) while strengthening the lesser strong (hydrophobic) interactions. Lysozyme is atypical in the breadth of its crystallization conditions; many proteins only crystallize under narrowly defined conditions, pointing to the criticality of the empirical balancing process. Lack of a singularly defined association pathway leads to formation of multiple species, i.e., amorphous precipitation. Weak interactions, such as hydrogen bonds, are promiscuous, serving to strengthen rather than define specific interactions. Participation in an interaction sequesters that surface from subsequent interactions, and we expect the strongest bonds to form first. When two molecules self associate the resulting species will have an axis of symmetry. Subsequent interactions between two associated species having equivalent interactions will also have symmetry. Only a few unique sets of interactions are required to give any of the commonly found space groups for monomeric proteins. This model and what it suggests will be discussed.

Pusey, Marc L.↗
DOE OSTI2021

Geometrical Frustration and Defect Formation in Growth of Colloidal Nanoparticle Crystals on a Cylinder: Implications for Assembly of Chiral Nanomaterials

Using a combination of experiment and simulation, we study how two-dimensional (2D) crystals of colloidal nanoparticles grow on cylindrical substrates. The cylindrical geometry allows us to examine growth in the absence of Gaussian curvature but in the presence of a closure constraint - the requirement that a crystal loops back onto itself. In some cases, this constraint results in structures that have been observed previously in theory and nonequilibrium packing experiments: chiral crystals and crystals with linear defects known as "line slips". More generally, though, the structures we see differ from those that have been observed: the line slips are kinked and contain partial vacancies. We show that these structures arise because the cylinder changes how the crystal grows. After a crystal wraps around the cylinder and touches itself, it must grow preferentially along the cylinder axis. As a result, crystals with a chiral line slip tend to trap partial vacancies. Indeed, we find that line slips that are less aligned with the cylinder axis incorporate more partial vacancies on average than the ones that are more aligned. Here, these results show that crystal growth on a cylinder is frustrated by the closure requirement, a finding that may shed some light on the assembly of biological nanosystems such as tobacco mosaic virus and might inform ways to fabricate chiral optical nanomaterials.

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

Many paths, similar destinations: viruses and bacterial microcompartments form polyhedra inside cells

A large number of biological entities assemble into icosahedral structures, and these are ubiquitous throughout nature. Examples include eukaryotic and prokaryotic viral capsids and more recently discovered bacterial microcompartments. Viral capsids and bacterial microcompartments are both composed of pentameric and hexameric subunits; however, they differ in the type of cargo they encapsulate: nucleic acid or protein. Also, both depart from strict icosahedral symmetry: while this is less common in viruses, among bacterial microcompartments, diverse and heterogeneous polyhedra are common. We review shared principles and key distinctions between the self-directed assembly of various icosahedral architectures and their polyhedral variants in nature and explore the concept that there are multiple paths, influenced by their cargo, to arriving at similar protein cage morphologies.

bacterial microcompartments↗
DOE OSTI2022

Two–Dimensional Excitonic Networks Directed by DNA Templates as an Efficient Model Light–Harvesting and Energy Transfer System

Photosynthetic organisms organize discrete light-harvesting complexes into large-scale networks to facilitate efficient light collection and utilization. Inspired by nature, herein, synthetic DNA templates were used to direct the formation of dye aggregates with a cyanine dye, K21, into discrete branched photonic complexes, and two-dimensional (2D) excitonic networks. The DNA templates ranged from four-arm DNA tiles, ≈10 nm in each arm, to 2D wireframe DNA origami nanostructures with different geometries and varying dimensions up to 100×100 nm. These DNA-templated dye aggregates presented strongly coupled spectral features and delocalized exciton characteristics, enabling efficient photon collection and energy transfer. Compared to the discrete branched photonic systems templated on individual DNA tiles, the interconnected excitonic networks showed approximately a 2-fold increase in energy transfer efficiency. Lastly, this bottom-up assembly strategy paves the way to create 2D excitonic systems with complex geometries and engineered energy pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2002

A Proposed Model for Protein Crystal Nucleation and Growth

How does one take a molecule, strongly asymmetric in both shape and charge distribution, and assemble it into a crystal? We propose a model for the nucleation and crystal growth process for tetragonal lysozyme, based upon fluorescence, light, neutron, and X-ray scattering data, size exclusion chromatography experiments, dialysis kinetics, AFM, and modeling of growth rate data, from this and other laboratories. The first species formed is postulated to be a 'head to side' dimer. Through repeating associations involving the same intermolecular interactions this grows to a 4(sub 3) helix structure, that in turn serves as the basic unit for nucleation and subsequent crystal growth. High salt attenuates surface charges while promoting hydrophobic interactions. Symmetry facilitates subsequent helix-helix self-association. Assembly stability is enhanced when a four helix structure is obtained, with each bound to two neighbors. Only two unique interactions are required. The first are those for helix formation, where the dominant interaction is the intermolecular bridging anion. The second is the anti-parallel side-by-side helix-helix interaction, guided by alternating pairs of symmetry related salt bridges along each side. At this stage all eight unique positions of the P4(sub3)2(sub 1),2(sub 1) unit cell are filled. The process is one of a) attenuating the most strongly interacting groups, such that b) the molecules begin to self-associate in defined patterns, so that c) symmetry is obtained, which d) propagates as a growing crystal. Simple and conceptually obvious in hindsight, this tells much about what we are empirically doing when we crystallize macromolecules. By adjusting the growth parameters we are empirically balancing the intermolecular interactions, preferentially attenuating the dominant strong (for lysozyme the charged groups) while strengthening the lesser strong (hydrophobic) interactions. In the general case for proteins the lack of a singularly defined association pathway may lead to formation of multiple species, i.e., amorphous precipitation. Weak interactions, such as hydrogen bonds, are promiscuous, serving to strengthen rather than define specific interactions. Participation in an interaction sequesters that surface from subsequent interactions, and we expect the strongest bonds to form first. This model, its basis, how it fits into the currently understood osmotic second virial coefficient approach to crystallization, and what it suggests will be discussed.

Pusey, Marc↗
DOE OSTI2020

Engineering the atomic structure of sequence-defined peptoid polymers and their assemblies

Peptoids are a family of sequence-defined, non-natural biomimetic polymers which show excellent properties including good chemical and enzymatic stability and high structural tunability. The solid-phase submonomer synthesis method allows precise control over the identity and sequence of chemically diverse side chains, enabling the atomic engineering of their chemical structures for a variety of applications. This unprecedented level of structural control enables access to atomically defined three-dimensional chain conformations and assemblies, facilitating the design and optimization of a variety of nanoscale architectures that can function in biology and materials science. In order to approach the rational design of peptoid materials in a more predictive and precise manner, it is crucial to fully understand how chemical information, in the form of the monomer sequence, encodes their folding and assembly into structurally defined, functional 3D shapes. Furthermore, this perspective focuses on recent studies into the atomic engineering of peptoid nanostructures by examining the impact of sequence variations on their secondary and three-dimensional structures, as well as their functional properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Skeletides: A Modular, Simplified Physical Model of Protein Secondary Structure

Three-dimensional (3D) models are essential for visualization and conceptual understanding of complex architectures such as protein structure. Although there is a plethora of software platforms that allow digital depictions of protein structure at an atomic level in silico, physical models are needed to convey an intuitive understanding of biomolecular architecture. However, it is a challenge to represent all the relevant features of proteins in a single physical model due to their sheer structural complexity. Here, we describe a modular protein model that focuses only on representation of the secondary structure—the underlying structural skeleton. The simplified model consists of amino acid units, which can be linked together to reproduce the two most fundamental structural features of protein secondary structure: the relative positions of the amino acid alpha carbon atoms, and the intra-main chain hydrogen bonding pattern. We use 3D printing and magnets to create a set of three modular amino acid building blocks, which when linked together into a chain, can faithfully represent alpha helices, beta sheets, and turns. These simple to make models can be used to quickly assemble the alpha carbon trace of an entire protein domain, which conveys a tactile experience of the complexity of protein skeletal architecture. These models highlight the modularity of protein structure: where a single structural unit, the amino acid, can be linked together to form a larger, regular secondary structure. These models also have a propensity to spontaneously organize into alpha helices and beta sheets, as demonstrated by their ability to autonomously assemble when placed in a circulating water tank. These models provide a missing educational tool to expand knowledge of protein structure, foster deeper insight into protein folding, and inspire greater interest in biomacromolecular architecture.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Role of Cations in the Cation-Driven Assembly Process and their Effect on the Charge Storage Properties of Bilayered Vanadium Oxide and Reduced Graphene Oxide Heterostructures in Alkali Ion Systems

Exfoliated δ-Li x V 2 O 5 ·nH 2 O (ex-LVO) and reduced graphene oxide (rGO) heterostructures were constructed using different assembling cations (i.e., Li⁺, Na⁺, and K⁺ ions). The ex-LVO and rGO nanoflakes were stacked together using a concentrated chloride solution of each assembling cation and vacuum annealed at 200 °C to form three distinct two-dimensional (2D) layered architectures. X-ray diffraction and thermogravimetric analysis confirmed that the assembling ions can control the interlayer spacing of the bilayered vanadium oxide (BVO) phase as well as impact the crystallographic water content, which in turn affects the electrochemical performance. Scanning electron microscopy, scanning transmission electron microscopy (STEM), electron energy-loss spectroscopy (EELS), and X-ray photoelectron spectroscopy confirmed that a 2D heterointerface formed between LVO and rGO and that the cations used to assemble the heterostructure are trapped in the interlayer BVO region. High-resolution STEM imaging also showed the rGO dispersion throughout the LVO layers. Moreover, STEM-EELS identified a V 2 O 3 phase that forms along the rGO interface and can stabilize the materials during cycling. A charge storage mechanism analysis, combined with the galvanostatic intermittent titration technique, found that increased interlayer spacings of the BVO phase and using the assembling cations to define intercalation sites for identical charge-carrying ions lead to improved ion diffusion and increased capacities during cycling. Therefore, the Li⁺ and Na⁺ ion assembled heterostructures showed improved charge-carrying ion diffusion and charge storage capacities in each of their respective charge storage systems (i.e., Li-ion and Na-ion half-cells). In total, the cation used for heterostructure assembly can modify the final material structure and tailor the ion diffusion and charge storage capacity to tune its properties for the desired electrochemical system using a variety of 2D materials.

25 ENERGY STORAGE↗
DOE OSTI2021

Intramolecular structure and dynamics in computationally designed peptide-based polymers displaying tunable chain stiffness

Here, polymers assembled using computationally designed coiled coil bundlemers display tunable stiffness via control of interbundlemer covalent connectivity as confirmed using small-angle neutron scattering. Neutron spin echo spectroscopy reveals that rigid rod polymers show a decay rate Γ~Q 2 (Q is the scattering vector) expected of straight cylinders. Semirigid polymers assembled using bundlemers linked via 4-armed organic linker show flexible segmental dynamics at mid-Q and Γ~Q 2 behavior at high Q. The results give insight into linker flexibility-dependent interbundlemer dynamics in the hybrid polymers.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Electrostatic co-assembly of nanoparticles with oppositely charged small molecules into static and dynamic superstructures

Coulombic interactions can be used to assemble charged nanoparticles into higher-order structures, but the process requires oppositely charged partners that are similarly sized. The ability to mediate the assembly of such charged nanoparticles using structurally simple small molecules would greatly facilitate the fabrication of nanostructured materials and harnessing their applications in catalysis, sensing and photonics. Here we show that small molecules with as few as three electric charges can effectively induce attractive interactions between oppositely charged nanoparticles in water. These interactions can guide the assembly of charged nanoparticles into colloidal crystals of a quality previously only thought to result from their co-crystallization with oppositely charged nanoparticles of a similar size. Transient nanoparticle assemblies can be generated using positively charged nanoparticles and multiply charged anions that are enzymatically hydrolysed into mono- and/or dianions. Overall, our findings demonstrate an approach for the facile fabrication, manipulation and further investigation of static and dynamic nanostructured materials in aqueous environments.

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

Kinetic Growth of Multicomponent Microcompartment Shells

An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Altogether, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.

defects↗
DOE OSTI2020

Hierarchical supramolecular assembly of a single peptoid polymer into a planar nanobrush with two distinct molecular packing motifs

Significance The preparation of hierarchical biomimetic nanostructures remains a challenging task. Bioinspired peptoid polymers offer a promising opportunity to encode assembly information within the component chains. Here, we report a one-pot preparation of planar nanobrush structures from poly(ethyleneglycol)- block -poly( N -octylglycine) based on tuning the interplay of crystallization and solvophobicity. Each nanobrush assembly is composed of two distinct structural domains, which form sequentially by control of the solution temperature, and contain distinct molecular packing motifs. Micellar intermediates first assemble into linear arrays at elevated temperature in a mesophase state, followed by lateral, crystallization-driven growth in a living manner upon cooling. Precise control over the nanobrush dimensions could be achieved. The structural tunability and excellent biocompatibility of polypeptoids offer great potential for nanomaterials inaccessible previously.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Topological Assembly of a Deployable Hoberman Flight Ring from DNA

Deployable geometries are finite auxetic structures that preserve their overall shapes during expansion and contraction. The topological behaviors emerge from intricately arranged elements and their connections. Despite the considerable utility of such configurations in nature and in engineering, deployable nanostructures have never been demonstrated. In this paper, a deployable flight ring, a simplified planar structure of Hoberman sphere is shown, using DNA origami. The DNA flight ring consists of topologically assembled six triangles in two layers that can slide against each other, thereby switching between two distinct (open and closed) states. The origami topology is a trefoil knot, and its auxetic reconfiguration results in negative Poisson’s ratios. This work shows the feasibility of deployable nanostructures, providing a versatile platform for topological studies and opening new opportunities for bioengineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Interfacial Assembly and Jamming of Soft Nanoparticle Surfactants into Colloidosomes and Structured Liquids

Nanoparticle surfactant (NPS) offers a powerful strategy to generate all-liquid constructs that integrate the inherent properties of the NPs into 3D architectures. In this report using the co-assembly of fluorescent polymeric nanoparticles and amine-functionalized polyhedral oligomeric silsesquioxane, the assembly and jamming behavior of a new type of NPS at the oil-water interface is uncovered. Unlike "solid" inorganic nanoparticles, "soft" polymeric nanoparticles can reorganize when jammed, leading to a relaxation and deformation of the interfacial assemblies, for example, the 3D printed sugar-coated haw stick-like liquid tubules. With NPS serving as emulsifiers, stable Pickering emulsions are prepared that can be converted into robust colloidosomes with pH responsiveness, showing numerous potential applications for encapsulation and controlled release.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Design of multi-scale protein complexes by hierarchical building block fusion

A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two classes of modular building blocks: designed helical repeat proteins (DHRs) and helical bundle oligomers (HBs). We first rigidly fuse DHRs to HBs to generate a large library of oligomeric building blocks. We then generate assemblies with cyclic, dihedral, and point group symmetries from these building blocks using architecture guided rigid helical fusion with new software named WORMS. X-ray crystallography and cryo-electron microscopy characterization show that the hierarchical design approach can accurately generate a wide range of assemblies, including a 43 nm diameter icosahedral nanocage. The computational methods and building block sets described here provide a very general route to de novo designed protein nanomaterials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Ferromagnetic liquid droplets with adjustable magnetic properties

Significance Structured functional liquids combine mechanical versatility of fluids with solid-state properties, such as ferromagnetism, and offer a route to synthesize and control magnetic liquids for adaptive liquid robotics. Studies on these intriguing materials are only in their nascent state, and a profound understanding of the physical state is still lacking. We use hydrodynamics experiments to probe how the magnetization of ferromagnetic liquid droplets, governed by the assembly and jamming of magnetic nanoparticles at liquid–liquid interfaces, and their response to external stimuli can be tuned by chemical, structural, and magnetic means. Our results highlight the leading role of structural short-range order on magnetic properties, which provide a path toward nano-patterning structured liquids.

36 MATERIALS SCIENCE↗