Structural ordering of the Plasmodium berghei circumsporozoite protein repeats by inhibitory antibody 3D11
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99 GENERAL AND MISCELLANEOUS↗
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Electron Tomography and Machine Learning for Understanding the Highly Ordered Structure of Leafhopper Brochosomes
Insects known as leafhoppers (Hemiptera: Cicadellidae) produce hierarchically structured nanoparticles known as brochosomes that are exuded and applied to the insect cuticle, thereby providing camouflage and anti-wetting properties to aid insect survival. Although the physical properties of brochosomes are thought to depend on the leafhopper species, the structure–function relationships governing brochosome behavior are not fully understood. Brochosomes have complex hierarchical structures and morphological heterogeneity across species, due to which a multimodal characterization approach is required to effectively elucidate their nanoscale structure and properties. In this work, we study the structural and mechanical properties of brochosomes using a combination of atomic force microscopy (AFM), electron microscopy (EM), electron tomography, and machine learning (ML)-based quantification of large and complex scanning electron microscopy (SEM) image data sets. This suite of techniques allows for the characterization of internal and external brochosome structures, and ML-based image analysis methods of large data sets reveal correlations in the structure across several leafhopper species. Our results show that brochosomes are relatively rigid hollow spheres with characteristic dimensions and morphologies that depend on leafhopper species. Nanomechanical mapping AFM is used to determine a characteristic compression modulus for brochosomes on the order of 1–3 GPa, which is consistent with crystalline proteins. Altogether, this work provides an improved understanding of the structural and mechanical properties of leafhopper brochosomes using a new set of ML-based image classification tools that can be broadly applied to nanostructured biological materials.
Chemical structure↗
Continuous chemical redistribution following amorphous-to-crystalline structural ordering in a Zr-Cu-Al bulk metallic glass
Not Available
Wu, Xuelian (ORCID:0000000175372325)↗
Spatially resolved structural order in low-temperature liquid electrolyte
Determining the degree and the spatial extent of structural order in liquids is a grand challenge. Here, we are able to resolve the structural order in a model organic electrolyte of 1 M lithium hexafluorophosphate (LiP 6 ) dissolved in 1:1 (v/v) ethylene carbonate:diethylcarbonate by developing an integrated method of liquid-phase transmission electron microscopy (TEM), cryo-TEM operated at -30°C, four-dimensional scanning TEM, and data analysis based on deep learning. This study reveals the presence of short-range order (SRO) in the high–salt concentration domains of the liquid electrolyte from liquid phase separation at the low temperature. Molecular dynamics simulations suggest the SRO originates from the Li + - (PF 6 - ) n (n > 2) local structural order induced by high LiP 6 salt concentration.
42 ENGINEERING↗
Analysis of noise produced by an orderly structure of turbulent jets
The orderly structure which has been observed recently by numerous researchers within the transition region of subsonic turbulent jets is analyzed to reveal its noise-producing potential. For a circular jet, this structure is molded as a train of toroidal vortex rings which are formed near the jet exit and propagate downstream. The noise produced by the model is evaluated from a reformulation of Lighthill's expression for the far-field acoustic density, which emphasizes the importance of the vorticity within the turbulent flow field. It is shown that the noise production occurs mainly close to the jet exit and depends primarily upon temporal changes in the toroidal radii. The analysis suggests that the process of formation of this regular structure may also be an important contribution of the high-frequency jet noise. These results may be helpful in the understanding of jet-noise generation and in new approaches to jet-noise suppression.
Hardin, J. C.↗
PyLRO: A Python calculator for analyzing long-range structural order
We present PyLRO, an open-source Python calculator designed to detect, quantify, and display long-range order in periodic structures. The program’s design methodology, workflow, and approach to order quantification are described and demonstrated using a simple toy model. Additionally, we apply PyLRO to a series of metastable AlPO 4 structural intermediates from a prior high-pressure study, demonstrating how to compute and visualize structural order in all directions on a Miller sphere. We further highlight the program’s capabilities through a high-throughput analysis of structural patterns in the pressure-induced amorphization of AlPO 4 , revealing atomistic insights into specific energy regions of massive amorphous structures. These results suggest that PyLRO can be a valuable tool for investigating crystal–amorphous transition in materials research.
36 MATERIALS SCIENCE↗
Structurally ordered nanoparticles, methods and applications
Embodiments provide a nanoparticle and a method for preparing the nanoparticle, as well as a membrane that includes the nanoparticle and a fuel cell that includes the membrane. The method comprises a thermal treatment method that provides from a nanoparticle comprising a structurally disordered material the nanoparticle comprising: (1) a structurally ordered core comprising a first material; and (2) a shell surrounding and further structurally aligned with the structurally ordered core and comprising a second material different from the first material. Particularly desirable is a nanoparticle comprising a Pt3Co@Pt/C structurally ordered core-shell composition supported upon a carbon support.
Abruna, Hector D.↗
Disentangling Coexisting Structural Order Through Phase Lock-In Analysis of Atomic-Resolution STEM Data
As a real-space technique, atomic-resolution STEM imaging contains both amplitude and geometric phase information about structural order in materials, with the latter encoding important information about local variations and heterogeneities present in crystalline lattices. Such phase information can be extracted using geometric phase analysis (GPA), a method which has generally focused on spatially mapping elastic strain. Here we demonstrate an alternative phase demodulation technique and its application to reveal complex structural phenomena in correlated quantum materials. As with other methods of image phase analysis, the phase lock-in approach can be implemented to extract detailed information about structural order and disorder, including dislocations and compound defects in crystals. Extending the application of this phase analysis to Fourier components that encode periodic modulations of the crystalline lattice, such as superlattice or secondary frequency peaks, we extract the behavior of multiple distinct order parameters within the same image, yielding insights into not only the crystalline heterogeneity but also subtle emergent order parameters such as antipolar displacements. When applied to atomic-resolution images spanning large (~0.5 × 0.5 μm 2 ) fields of view, this approach enables vivid visualizations of the spatial interplay between various structural orders in novel materials.
74 ATOMIC AND MOLECULAR PHYSICS↗
Enumeration as a Tool for Structure Solution: A Materials Genomic Approach to Solving the Cation-Ordered Structure of Na 3 V 2 (PO 4 ) 2 F 3
While powder diffraction methods are routinely utilized to optimize structural models for compounds whose crystal structures are known, the determination of unknown structures is far more challenging. When the unknown structure is large, structure solution can become a virtually intractable problem using standard structure solution methodologies, especially when the space group cannot be unambiguously resolved. One such system is the promising Na-ion battery cathode material Na 3 V 2 (PO 4 ) 2 F 3 whose high temperature and room temperature structures were previously solved, but whose more complex low-temperature structure could not be determined. Here, a novel materials genomic approach is demonstrated for the solution of the unknown 100 K structure of Na 3 V 2 (PO 4 ) 2 F 3 in which enumeration methods are first used to generate a large number (~3,000) of trial structures based on plausible orderings of Na ions and then automated Rietveld refinements are carried out to optimize each of these trial structures. Based on both the analysis of the ensemble of optimized trial structures and the density functional theory energy minimization of selected trial structures, the 100 K structure of Na 3 V 2 (PO 4 ) 2 F 3 is best described as belonging to the space group A2 1 am with unit cell dimensions of a = 9.01928(4), b = 27.1379(1), c = 10.73307(5). The 100 K unit cell has a large volume of 2627.07(2) Å 3 with Z = 12 and 33 independent crystallographic sites (9 Na, 3 V, 3 P, 12 O, and 6 F) that is 3x and 6x larger than the room- and high-temperature polymorphs of this phase, respectively. Finally, the novel methods described here will be generally applicable for the solution of the complex cation-ordered structures that commonly occur for battery materials.
36 MATERIALS SCIENCE↗
NMR Spectroscopy for Protein Higher Order Structure Similarity Assessment in Formulated Drug Products
Peptide and protein drug molecules fold into higher order structures (HOS) in formulation and these folded structures are often critical for drug efficacy and safety. Generic or biosimilar drug products (DPs) need to show similar HOS to the reference product. The solution NMR spectroscopy is a non-invasive, chemically and structurally specific analytical method that is ideal for characterizing protein therapeutics in formulation. However, only limited NMR studies have been performed directly on marketed DPs and questions remain on how to quantitively define similarity. Here, NMR spectra were collected on marketed peptide and protein DPs, including calcitonin-salmon, liraglutide, teriparatide, exenatide, insulin glargine and rituximab. The 1D 1 H spectral pattern readily revealed protein HOS heterogeneity, exchange and oligomerization in the different formulations. Principal component analysis (PCA) applied to two rituximab DPs showed consistent results with the previously demonstrated similarity metrics of Mahalanobis distance (D M ) of 3.3. The 2D 1 H- 13 C HSQC spectral comparison of insulin glargine DPs provided similarity metrics for chemical shift difference (Δδ) and methyl peak profile, i.e., 4 ppb for 1 H, 15 ppb for 13 C and 98% peaks with equivalent peak height. Finally, 2D 1 H- 15 N sofast HMQC was demonstrated as a sensitive method for comparison of small protein HOS. The application of NMR procedures and chemometric analysis on therapeutic proteins offer quantitative similarity assessments of DPs with practically achievable similarity metrics.
59 BASIC BIOLOGICAL SCIENCES↗
Higher-order structure of rRNA
A comparative search for phylogenetically covarying basepair replacements within potential helices has been the only reliable method to determine the correct secondary structure of the 3 rRNAs, 5S, 16S, and 23S. The analysis of 16S from a wide phylogenetic spectrum, that includes various branches of the eubacteria, archaebacteria, eucaryotes, in addition to the mitochondria and chloroplast, is beginning to reveal the constraints on the secondary structures of these rRNAs. Based on the success of this analysis, and the assumption that higher order structure will also be phylogenetically conserved, a comparative search was initiated for positions that show co-variation not involved in secondary structure helices. From a list of potential higher order interactions within 16S rRNA, two higher-order interactions are presented. The first of these interactions involves positions 570 and 866. Based on the extent of phylogenetic covariation between these positions while maintaining Watson-Crick pairing, this higher-order interaction is considered proven. The other interaction involves a minimum of six positions between the 1400 and 1500 regions of the 16S rRNA. Although these patterns of covariation are not as striking as the 570/866 interaction, the fact that they all exist in an anti-parallel fashion and that experimental methods previously implicated these two regions of the molecule in tRNA function suggests that these interactions be given serious consideration.
Gutell, R. R.↗
Ballistic ion transport through hierarchically-ordered-structure polymer binder
Achieving ballistic ion transport in a mixed electronic-ionic conductive polymer, its hierarchically ordered structure (HOS) facilitates ion diffusion and results in solid-state Li + conductivity in the range of 10 −4 to 10 −3 S cm −1 from −20 to 70 °C.
Li, Defu [Energy storage and Distributed Resources↗
Discrete integration of continuous Kalman filtering equations for time invariant second-order structural systems
A general form for the first-order representation of the continuous second-order linear structural-dynamics equations is introduced to derive a corresponding form of first-order continuous Kalman filtering equations. Time integration of the resulting equations is carried out via a set of linear multistep integration formulas. It is shown that a judicious combined selection of computational paths and the undetermined matrices introduced in the general form of the first-order linear structural systems leads to a class of second-order discrete Kalman filtering equations involving only symmetric sparse N x N solution matrices.
Park, K. C.↗
Charge Carrier Induced Structural Ordering And Disordering in Organic Mixed Ionic Electronic Conductors
Operational stability underpins the successful application of organic mixed ionic-electronic conductors (OMIECs) in a wide range of fields, including biosensing, neuromorphic computing, and wearable electronics. Here in this work, both the operation and stability of a p-type OMIEC material of various molecular weights are investigated. Electrochemical transistor measurements reveal that device operation is very stable for at least 300 charging/discharging cycles independent of molecular weight, provided the charge density is kept below the threshold where strong charge–charge interactions become likely. When electrochemically charged to higher charge densities, an increase in device hysteresis and a decrease in conductivity due to a drop in the hole mobility arising from long-range microstructural disruptions are observed. By employing operando X-ray scattering techniques, two regimes of polaron-induced structural changes are found: 1) polaron-induced structural ordering at low carrier densities, and 2) irreversible structural disordering that disrupts charge transport at high carrier densities, where charge–charge interactions are significant. These operando measurements also reveal that the transfer curve hysteresis at high carrier densities is accompanied by an analogous structural hysteresis, providing a microstructural basis for such instabilities. This work provides a mechanistic understanding of the structural dynamics and material instabilities of OMIEC materials during device operation.
36 MATERIALS SCIENCE↗
Formulation of full state feedback for infinite order structural systems
The estimation of exact displacement and displacement rate feedback kernels from finite dimensional control solutions based on finite element structural models is discussed. These kernels are then transformed to equivalent curvature and curvature rate feedback kernels. These curvature kernels are augmented with single point displacement and rotation feedback to account for rigid body motions. A growing class of sensors known as area-averaging sensors is used to measure the curvature and curvature rate state functions. The output of area-averaging sensors equals the convolution of all structural curvature states with the spatial sensitivity function of the sensors. Transforming the discrete feedback gains into continuous feedback kernels and employing area-averaging sensors make it possible to implement full state feedback for infinite order structural systems.
Miller, David W.↗
3D Exact Analytical Solutions of Two-fluid Plasma, Magnetohydrodynamics, and Neutral Fluid Equations for the Creation of Ordered Structures as well as Jet-like Flows
The 3D exact analytical solutions of ideal two-fluid plasma, single-fluid plasma, and neutral fluid equations have been found using physically justifiable assumptions. Surprisingly these solutions satisfy all nonlinearities in the systems. It is pointed out that these solutions explain the fundamental mechanism behind the creation of a vast variety of ordered structures in plasmas and fluids. In the limiting case of 2D dependence of fields, the theoretical model for plasma is applied to explain the formation of spicules in the solar chromosphere. It is pointed out that the main contribution of electron (ion) baroclinic vectors is to produce vorticity in the plasma, and that magnetic field generation is coupled with the flow of both electrons and ions.
79 ASTRONOMY AND ASTROPHYSICS↗
Graph characterization of higher-order structure in atmospheric chemical reaction mechanisms
Atmospheric chemical reactions play an important role in air quality and climate change. While the structure and dynamics of individual chemical reactions are fairly well understood, the emergent properties of the entire atmospheric chemical system, which can involve many different species that participate in many different reactions, are not well described. In this work, we leverage graph-theoretic techniques to characterize patterns of interaction (“motifs”) in three different representations of gas-phase atmospheric chemistry, termed “chemical mechanisms.” These widely used mechanisms, the master chemical mechanism, the GEOS-Chem mechanism, and the Super-Fast mechanism, vary dramatically in scale and application, but they all generally aim to simulate the abundance and variability of chemical species in the atmosphere. This motif analysis quantifies the fundamental patterns of interaction within the mechanisms, which are directly related to their construction. For example, the gas-phase chemistry in the very small Super-Fast mechanism is entirely composed of bimolecular reactions, and its motif distribution matches that of an individual bimolecular reaction well. The larger and more complex mechanisms show emergent motif distributions that differ strongly from any specific reaction type, consistent with their complexity. The proposed motif analysis demonstrates that while these mechanisms all have a similar design goal, their higher-order structure of interactions differs strongly and thus provides a novel set of tools for exploring differences across chemical mechanisms.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗