From All-Printed 2D Patterns to Free-Standing 3D Structures: Controlled Buckling and Selective Bonding
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Materials Science↗
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Parton distributions and lattice-QCD calculations: Toward 3D structure
The strong force which binds hadrons is described by the theory of quantum chromodynamics (QCD). Determining the character and manifestations of QCD is one of the most important and challenging outstanding issues necessary for a comprehensive understanding of the structure of hadrons. Within the context of the QCD parton picture, the parton distribution functions (PDFs) have been remarkably successful in describing a wide variety of processes. However, these PDFs have generally been confined to the description of collinear partons within the hadron. New experiments and facilities provide the opportunity to additionally explore the transverse structure of hadrons which is described by generalized parton distributions (GPDs) and transverse-momentum-dependent parton distribution functions (TMD PDFs). In our previous report Lin et al. (2018), we compared and contrasted the two main approaches used to determine the collinear PDFs: the first based on perturbative QCD factorization theorems, and the second based on lattice-QCD calculations. In the present report, we provide an update of recent progress on the collinear PDFs, and also expand the scope to encompass the generalized PDFs (GPDs and TMD PDFs). We review the current state of the various calculations, and consider what new data might be available in the near future. We also examine how a shared effort can foster dialog between the PDF and lattice-QCD communities, and yield improvements for these generalized PDFs.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination
To understand the dynamic structure–function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
3D structures and methods therefor
Aspects of the disclosure are directed to methods and/or apparatuses involving one or more of a conductive polymer, deposition of a conductive polymer and 3D (three-dimensional) printing of a continuous bead of material. As may be implemented in accordance with one or more embodiments characterized herein, a 3D structure is formed as follows. A stacked layer is formed by depositing a continuous bead of material along an uninterrupted path that defines a first layer of the 3D structure. A sidewall of the 3D structure is formed with opposing surfaces respectively defined by successive stacked layers of the 3D structure by, for each stacked layer (including the first layer), depositing the continuous bead of material along the path and with a surface thereof in contact with a surface of the continuous bead of material of an adjacent one of the stacked layers.
Nellis, Gregory↗
Kirigami-Inspired Self-Assembly of 3D Structures
Self-assembly of 3D structures introduce an attractive and scalable route to realize reconfigurable and functionally capable mesoscale devices without human intervention. A common approach for achieving this is to utilize stimuli-responsive folding of hinged structures, which requires the integration of different materials and/or geometric arrangements along the hinges. It is also demonstrated that the inclusion of Kirigami cuts in planar, hingeless bilayer thin sheets can be used to produce complex 3D shapes in an on-demand manner. Nonlinear finite element models are developed to elucidate the mechanics of shape morphing in bilayer thin sheets and verify the predictions through swelling experiments of planar, millimeter-scaled PDMS (polydimethylsiloxane) bilayers in organic solvents. Building upon the mechanistic understandings, The transformation of Kirigami-cut simple bilayers into 3D shapes such as letters from the Roman alphabet (to make “ADVANCED FUNCTIONAL MATERIALS”) and open/closed polyhedral architectures is experimentally demonstrated. A possible application of the bilayers as tether-less optical metamaterials with dynamically tunable light transmission and reflection behaviors is also shown. As the proposed mechanistic design principles could be applied to a variety of materials, this research broadly contributes toward the development of smart, tetherless, and reconfigurable multifunctional systems.
36 MATERIALS SCIENCE↗
High capacity 3D structured tin-based electroplated Li-ion battery anodes
3D structured porous electrodes have been considered as a possible solution for accommodating the volume change of alloying lithium ion battery anode materials during cycling. However, lab-scale porous electrodes tend to be thin, and the loading of the activity materials is also small, the combination of which results in electrodes with impractically low areal and volumetric capacities. In this work, we develop a high areal and volumetric capacity 3D-structured Sn/C anode by using a two steps electroplating process. An electrode with a 20% v/v Sn loading exhibits a high volumetric/areal capacity of similar to 879 mA h/cm 3 /6.59 mA h/cm 2 after 100 cycles at 0.5 C and a good rate performance of about 750 mA h/cm 3 and 5.5 mA h/cm 2 (delithiation) at 10 C in a half-cell configuration. The 3D Sn/C anode also shows good compatibility with a commercial LCO cathode in a full cell configuration.
25 ENERGY STORAGE↗
Highly Enhanced Luminescence Performance of LEDs via Controllable Layer‐Structured 3D Photonic Crystals and Photonic Crystal Beads
Abstract Controllable layer‐structured 3D photonic crystals (PCs) are prepared using the combination of the Langmuir–Blodgett (LB) technique and layer‐by‐layer stacking method. They are used for research into the influence of the number of the layers on the enhancement of the efficiency of light emission from light‐emitting diodes (LEDs) and quantum dots (QDs). The luminescence properties of blue, green, and white LEDs are improved dramatically while applying such controllable layer‐structured 3D PCs as reflectors and the enhancement efficiencies are shown to increase with PC thickness. In addition, the fluorescence intensity increases 7.8‐fold and 5.4‐fold for red and green QDs, respectively, and the fluorescence intensity can be accurately controlled by using PCs with different layers. In addition, PC beads with yellow and red photonic bandgaps are used to improve the luminescence of a white LED with angle‐independent enhancement. These beads are simply doped into the phosphor without any other treatment. Interestingly, the light intensity of the PC bead based LED is remarkably enhanced. These quantized enhanced effect of light intensity on the thickness of PC layers, along with new generation of PC bead based LED, might offer a strategy for designing high brightness LEDs with energy‐saving performance.
Tian, Yu↗
IgG Antibody 3D Structures and Dynamics
Antibodies are vital for human health because of their ability to function as nature’s drugs by protecting the body from infection. In recent decades, antibodies have been used as pharmaceutics for targeted therapy in patients with cancer, autoimmune diseases, and cardiovascular diseases. Capturing the dynamic structure of antibodies and characterizing antibody fluctuation is critical for gaining a deeper understanding of their structural characteristics and for improving drug development. Current techniques for studying three-dimensional (3D) structural heterogeneity and variability of proteins have limitations in ascertaining the dynamic structural behavior of antibodies and antibody-antigen complexes. Here, we review current techniques used to study antibody structures with a focus on the recently developed individual-particle electron tomography (IPET) technique. IPET, as a particle-by-particle methodology for 3D structural characterization, has shown advantages in studying structural variety and conformational changes of antibodies, providing direct imaging data for biomolecular engineering to improve development and clinical application of synthetic antibodies.
antibody dynamics↗
Polyhedral 3D structure of human plasma very low density lipoproteins by individual particle cryo-electron tomography
Human VLDLs assembled in the liver and secreted into the circulation supply energy to peripheral tissues. VLDL lipolysis yields atherogenic LDLs and VLDL remnants that strongly correlate with CVD. Although the composition of VLDL particles has been well-characterized, their 3D structure is elusive because of their variations in size, heterogeneity in composition, structural flexibility, and mobility in solution. Here, we employed cryo-electron microscopy and individual-particle electron tomography to study the 3D structure of individual VLDL particles (without averaging) at both below and above their lipid phase transition temperatures. The 3D reconstructions of VLDL and VLDL bound to antibodies revealed an unexpected polyhedral shape, in contrast to the generally accepted model of a spherical emulsion-like particle. The smaller curvature of surface lipids compared with HDL may also reduce surface hydrophobicity, resulting in lower binding affinity to the hydrophobic distal end of the N-terminal β-barrel domain of cholesteryl ester transfer protein (CETP) compared with HDL. The directional binding of CETP to HDL and VLDL may explain the function of CETP in transferring TGs and cholesteryl esters between these particles. This first visualization of the 3D structure of VLDL could improve our understanding of the role of VLDL in atherogenesis.
59 BASIC BIOLOGICAL SCIENCES↗
The relation between lignin sequence and its 3D structure
Background: Lignin, the second most abundant biopolymer on earth, plays a major structural role in plants, conferring mechanical strength and regulating water conduction. Understanding the three-dimensional structure of lignin is important for fundamental reasons as well as engineering plants towards lignin valorization. Lignin lacks a specific primary sequence, making its average chemical composition the focus of most recent studies. However, it remains unclear whether the 3D structure of lignin molecules depends on their sequence. Methods: In this work, we performed all-atom molecular dynamics simulation of three S/G-lignin molecules with the same average composition but different sequence. Results: A detailed statistical analysis of the radius of gyration and relative shape anisotropy reveals that the lignin sequence has no statistically significant effect on the global three-dimensional structure. We found however, that homopolymers of C-lignin with the same molecular weight have smaller radii of gyration than S/G-lignin. We attribute this to lower hydroxyl content of C-lignin, which makes it more compact and rigid. Conclusions: The 3D structure of lignin is influenced by the overall content of monomeric units and interunit linkages and not by its precise primary sequence. General Significance: Lignin is assumed to not have a well-defined primary structure. The results presented here demonstrate there are no significant differences in the global 3D structure of lignin molecules with the same average composition but different primary sequence.
59 BASIC BIOLOGICAL SCIENCES↗
Fabricating 3D Structures by Combining 2D Printing and Relaxation of Strain
This article describes the fabrication of elastomeric three-dimensional (3D) structures starting from two-dimensional (2D) sheets using a combination of direct-ink printing and relaxation of strain. These structures are fabricated in a two-step process: first, elastomeric inks are deposited as 2D structures on a stretched elastomeric sheet, and second, after curing of the elastomeric inks, relaxation of strain in the 2D sheet causes it to deform into a 3D shape. To predict bending of elastomeric objects fabricated with this technique, a simple mechanical model is developed. The strategy of using initially 2D materials to fabricate 3D structures offers four new features that complement digital fabrication techniques. (i) It provides a simple route to create shapes with complex curves, suspended features, and internal cavities. (ii) It is a faster method of fabricating some types of shapes than “conventional” 3D printing, because the features are printed in 2D. (iii) It forms surfaces that can be both smoother, and structured in a way that is not compatible with layer-by-layer processing. (iv) It forms structures that can be deformed reversibly after fabrication by reapplying strain. This paper demonstrates these features by fabrication of helices, structures inspired by cubes and tables, “pop-up” structures, and soft grippers.
36 MATERIALS SCIENCE↗
3D Printing of Supramolecular Polymer Hydrogels with Hierarchical Structure
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Sather, Nicholas A.↗
Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution
Most mosquito-borne flaviviruses, including Zika virus (ZIKV), Dengue virus (DENV), and West Nile virus (WNV), produce long non-coding subgenomic RNAs (sfRNAs) in infected cells that link to pathogenicity and immune evasion. Until now, the structural characterization of these lncRNAs remains limited. Here, we studied the 3D structures of individual and combined subdomains of sfRNAs, and visualized the accessible 3D conformational spaces of complete sfRNAs from DENV2, ZIKV, and WNV by small angle X-ray scattering (SAXS) and computational modeling. The individual xrRNA1s and xrRNA2s adopt similar structures in solution as the crystal structure of ZIKV xrRNA1, and all xrRNA1-2s form compact structures with reduced flexibility. While the DB12 of DENV2 is extended, the DB12s of ZIKV and WNV are compact due to the formation of intertwined double pseudoknots. All 3' stem-loops (3'SLs) share similar rod-like structures. Complete sfRNAs are extended and sample a large conformational space in solution. Our work not only provides structural insight into the function of flavivirus sfRNAs, but also highlights strategies of visualizing other lncRNAs in solution by SAXS and computational methods.
3D structure↗
Preference for a pressure-induced 3D structure after 1T-HfSe 2
Extensive crystal structure prediction searches provide evidence of two 3D structures with orthorhombic (Immm) and monoclinic (C2/m) space groups as reasonable candidates for the first pressure-induced phase of 1T-HfSe 2 . Our candidates are compared with two recent proposals that keep the 2D nature of the ambient conditions phase and display hexagonal (P6 3 /mmc) and monoclinic (C2/m) symmetry, although the latter has a different structure than our proposed C2/m phase. Both of these 2D-like structures are discarded based on simple thermodynamic and kinetic arguments that can be extended to explain the pressure-induced polymorphic sequence of other transition metal dichalcogenides. The computed observables of our orthorhombic phase are fully consistent with the experimental structural and Raman data observed at low and high-pressure.
36 MATERIALS SCIENCE↗
X-ray ptychographic tomography reveals buried 3D structural defects in metal halide perovskites
For the first of its kind, X-ray ptychographic imaging is utilized for probing metal halide perovskite crystals, revealing various 3D structural defects fully or partially buried underneath the perovskite surface. Here, this work demonstrates a powerful, non-intrusive 3D tomographic characterization method to illuminate the complete microstructure of perovskites for advanced energy applications.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Deconvoluting the influences of 3D structure on the performance of photoelectrodes for solar-driven water splitting
This study describes and demonstrates a systematic approach for deconvoluting the influences of 3D structure on photoelectrode performance.
bio-inspired, energy storage (including batteries ↗
Advanced NASA Earth Science Mission Concept for Vegetation 3D Structure, Biomass and Disturbance
Carbon in forest canopies represents about 85% of the total carbon in the Earth's aboveground biomass (Olson et al., 1983). A major source of uncertainty in global carbon budgets derives from large errors in the current estimates of these carbon stocks (IPCC, 2001). The magnitudes and distributions of terrestrial carbon storage along with changes in sources and sinks for atmospheric C02 due to land use change remain the most significant uncertainties in Earth's carbon budget. These uncertainties severely limit accurate terrestrial carbon accounting; our ability to evaluate terrestrial carbon management schemes; and the veracity of atmospheric C02 projections in response to further fossil fuel combustion and other human activities. Measurements of vegetation three-dimensional (3D) structural characteristics over the Earth's land surface are needed to estimate biomass and carbon stocks and to quantify biomass recovery following disturbance. These measurements include vegetation height, the vertical profile of canopy elements (i.e., leaves, stems, branches), andlor the volume scattering of canopy elements. They are critical for reducing uncertainties in the global carbon budget. Disturbance by natural phenomena, such as fire or wind, as well as by human activities, such as forest harvest, and subsequent recovery, complicate the quantification of carbon storage and release. The resulting spatial and temporal heterogeneity of terrestrial biomass and carbon in vegetation make it very difficult to estimate terrestrial carbon stocks and quantify their dynamics. Vegetation height profiles and disturbance recovery patterns are also required to assess ecosystem health and characterize habitat. The three-dimensional structure of vegetation provides habitats for many species and is a control on biodiversity. Canopy height and structure influence habitat use and specialization, two fundamental processes that modify species richness and abundance across ecosystems. Accurate and consistent 3D measurements of forest structure at the landscape scale are needed for assessing impacts to animal habitats and biodiversity following disturbance.
Ranson, K. Jon↗