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At least 523 records · Page 29

Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies

Neutralizing antibody responses to coronaviruses mainly target the receptor-binding domain (RBD) of the trimeric spike. Here, we characterized polyclonal immunoglobulin Gs (IgGs) and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their focus on RBD epitopes, recognition of alpha- and beta-coronaviruses, and contributions of avidity to increased binding/ neutralization of IgGs over Fabs. Using electron microscopy, we examined specificities of polyclonal plasma Fabs, revealing recognition of both S1 A and RBD epitopes on SARS-CoV-2 spike. Moreover, a 3.4 Å cryoelectron microscopy (cryo-EM) structure of a neutralizing monoclonal Fab-spike complex revealed an epitope that blocks ACE2 receptor binding. Modeling based on these structures suggested different potentials for inter-spike crosslinking by IgGs on viruses, and characterized IgGs would not be affected by identified SARS-CoV-2 spike mutations. Overall, our studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.

59 BASIC BIOLOGICAL SCIENCES↗

Functionalized Polymersomes from a Polyisoprene-Activated Polyacrylamide Precursor

Self-assembled polymer nanoparticles have tremendous potential in biomedical and environmental applications. For all applications, tailored polymer chemistries are critical. In this study, we demonstrate a precursor approach in which an activated, organic solvent-soluble block polymer precursor is modified through mild postpolymerization modifications to access new polymer structures. We synthesized and characterized poly(isoprene)-block-poly(di-Boc acrylamide) diblock polymers. This activated-acrylamide-based polymer was then reacted with amines or reductants in the absence of catalysts to yield the hydrophilic blocks polyacrylamide, poly(hydroxypropylene), and poly(N-ethyl acrylamide). The resulting amphiphilic block polymers self-assembled in water to form polymersomes, as confirmed by cryo-electron microscopy and confocal microscopy. The approach also enables simple functionalization with specialized ligands, which we demonstrated by tagging polymers with an amino-fluorophore and imaging by confocal microscopy. Here, we expect that the methodologies established in this study will open doors to new and useful solution nanostructures with surface chemistries that can be optimized for various applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular Simulation of Functionalized Covalent Organic Framework Membranes for Inorganic Salt Separation

Covalent organic frameworks (COFs) enable molecular-level design of nanochannels for selective separation in pressure-driven membrane processes. Through variation of building blocks and, subsequently, the pore structure and chemistry, membrane performance can be tailored. This study employs nonequilibrium molecular dynamics simulations to theoretically demonstrate the tunable selectivity of COF membranes through a bottom-up functionalization approach. Water and salt transport are evaluated for six β-ketoenamine-linked COFs with varying multilayer thicknesses. For the thinnest multilayer (0.64–0.72 nm), all COFs exhibit low sodium sulfate (Na 2 SO 4 ) rejection (55–66%). However, 20 stacked sheets (6.4–7.2 nm) provide 67–98% rejection, with the sulfonated COF providing the highest Na 2 SO 4 rejection. Analysis of time-resolved ion density profiles reveals that solute rejection is primarily governed by interfacial exclusion arising from pore size and functional group chemistry. Although increasing salt rejection compromises water permeance, the permeance of all COF membranes is at least two orders of magnitude greater than that of a commercially available nanofiltration membrane. Overall, this work guides the rational design of COF membranes for aqueous salt separation.

Nanofiltration↗

Effect of 60 Co γ-radiation on the tetrafluoroethylene/perfluoro(methyl vinyl ether) copolymer

The chemical and paramagnetic composition of the surface of the tetrafluoroethylene / perfluoro(methyl vinyl ether) copolymer (MFA) was investigated before and after γ-irradiation. The content of fluorine and carbon decreases at radiolysis of MFA, as well as the proportion of oxygen increases as a result of the oxidation reaction of radicals formed during γ-irradiation. The electron paramagnetic resonance (EPR) spectrum of the copolymer irradiated at 77 K contains the radicals ~CF 2 C∙FCF 2 ~ (1) and >CFOC∙F 2 (2). The absence of ~CF 2 C∙F 2 radicals, which can be formed at radiolytic rupture of the C—C bond of the copolymer main chain is associated with the effect of recombination of the resulting radical pair. The EPR spectrum of irradiated MFA at 300 K only recorded radical (1), which transform into peroxide radicals when air oxygen is introduced into the irradiated sample. Thermomechanical curves of native and radiolyzed MFA show three structural states of the amorphous block (glass, transition region, plateau of highly elastic deformation), as well as melting and molecular flow of the copolymer. The radio thermoluminescence curve shows five maxima associated with the emission of light during the recombination of stabilized ions and radicals during heating of the pre-irradiated MFA at 77 K. The temperature of the luminescence peak maximum at 336 K is close to the temperature of the onset of the devitrification of the chains of the amorphous block of MFA on the thermomechanical curve at 341 K. Irradiation leads to an increase in crystallinity of MFA. The heat of fusion of irradiated MFA on the Differential Scanning Calorimeter (DSC) curve is 50 % higher than the fusion heat of native copolymer. During the heating of γ-irradiated MFA, the relative content of COF molecules in the thermal decomposition products increases by an order of magnitude.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Porous Nanographenes, Graphene Nanoribbons, and Nanoporous Graphene Selectively Synthesized from the Same Molecular Precursor

In this study, we demonstrate a family of molecular precursors based on 7,10-dibromo-triphenylenes that can selectively produce different varieties of atomically precise porous graphene nanomaterials through the use of different synthetic environments. Upon Yamamoto polymerization of these molecules in solution, the free rotations of the triphenylene units around the C–C bonds result in the formation of cyclotrimers in high yields. In contrast, in on-surface polymerization of the same molecules on Au(111) these rotations are impeded, and the coupling proceeds toward the formation of long polymer chains. These chains can then be converted to porous graphene nanoribbons (pGNRs) by annealing. Correspondingly, the solution-synthesized cyclotrimers can also be deposited onto Au(111) and converted into porous nanographenes (pNGs) via thermal treatment. Thus, both processes start with the same molecular precursor and end with a porous graphene nanomaterial on Au(111), but the type of product, pNG or pGNR, depends on the specific coupling approach. We also produced extended nanoporous graphenes (NPGs) through the lateral fusion of highly aligned pGNRs on Au(111) that were grown at high coverage. The pNGs can also be synthesized directly in solution by Scholl oxidative cyclodehydrogenation of cyclotrimers. We demonstrate the generality of this approach by synthesizing two varieties of 7,10-dibromo-triphenylenes that selectively produced six nanoporous products with different dimensionalities. The basic 7,10-dibromo-triphenylene monomer is amenable to structural modifications, potentially providing access to many new porous graphene nanomaterials. We show that by constructing different porous structures from the same building blocks, it is possible to tune the energy band gap in a wide range.

25 ENERGY STORAGE↗

Broadly cross-reactive human antibodies that inhibit genogroup I and II noroviruses

The rational development of norovirus vaccine candidates requires a deep understanding of the antigenic diversity and mechanisms of neutralization of the virus. Here, we isolate and characterize a panel of broadly cross-reactive naturally occurring human monoclonal IgMs, IgAs and IgGs reactive with human norovirus (HuNoV) genogroup I or II (GI or GII). We note three binding patterns and identify monoclonal antibodies (mAbs) that neutralize at least one GI or GII HuNoV strain when using a histo-blood group antigen (HBGA) blocking assay. The HBGA blocking assay and a virus neutralization assay using human intestinal enteroids reveal that the GII-specific mAb NORO-320, mediates HBGA blocking and neutralization of multiple GII genotypes. The Fab form of NORO-320 neutralizes GII.4 infection more potently than the mAb, however, does not block HBGA binding. The crystal structure of NORO-320 Fab in complex with GII.4 P-domain shows that the antibody recognizes a highly conserved region in the P-domain distant from the HBGA binding site. Dynamic light scattering analysis of GII.4 virus-like particles with mAb NORO-320 shows severe aggregation, suggesting neutralization is by steric hindrance caused by multivalent cross-linking. Aggregation was not observed with the Fab form of NORO-320, suggesting that this clone also has additional inhibitory features.

59 BASIC BIOLOGICAL SCIENCES↗

The living interface between synthetic biology and biomaterial design

Recent far-reaching advances in synthetic biology have yielded exciting tools for the creation of new materials. Conversely, advances in the fundamental understanding of soft-condensed matter, polymers and biomaterials offer new avenues to extend the reach of synthetic biology. The broad and exciting range of possible applications have substantial implications to address grand challenges in health, biotechnology and sustainability. Despite the potentially transformative impact that lies at the interface of synthetic biology and biomaterials, the two fields have, so far, progressed mostly separately. This Perspective provides a review of recent key advances in these two fields, and a roadmap for collaboration at the interface between the two communities. Here we highlight the near-term applications of this interface to the development of hierarchically structured biomaterials, from bioinspired building blocks to 'living' materials that sense and respond based on the reciprocal interactions between materials and embedded cells.

59 BASIC BIOLOGICAL SCIENCES↗

A better way to define dark matter haloes

ABSTRACT Dark matter haloes have long been recognized as one of the fundamental building blocks of large-scale structure formation models. Despite their importance – or perhaps because of it! – halo definitions continue to evolve towards more physically motivated criteria. Here, we propose a new definition that is physically motivated, effectively unique, and parameter-free: ‘A dark matter halo is comprised of the collection of particles orbiting in their own self-generated potential’. This definition is enabled by the fact that, even with as few as ≈300 particles per halo, nearly every particle in the vicinity of a halo can be uniquely classified as either orbiting or infalling based on its dynamical history. For brevity, we refer to haloes selected in this way as physical haloes. We demonstrate that (1) the mass function of physical haloes is Press–Schechter, provided the critical threshold for collapse is allowed to vary slowly with peak height; and (2) the peak-background split prediction of the clustering amplitude of physical haloes is statistically consistent with the simulation data, with accuracy no worse than ≈5 per cent.

Astronomy & Astrophysics↗

Comparison of the Neutronic Performance of IRP-1 and IRP-2 at SNS

The Spallation Neutron Source (SNS) operated from start-up, in May 2006, through December, 2017 before replacing the Inner Reflector Plug (IRP). This component is the most costly and time-consuming “regular maintenance” replacement foreseen in the operation of the First Target Station (FTS). The IRP includes beryllium reflector blocks, steel and aluminum support structures, aluminum moderator vessels (which in turn include gadolinium and cadmium neutron poisons) and water coolant systems. The lifetime of this multi-million dollar component is driven by poison and decoupler burnup in moderator vessels. The moderators include these neutron poisons to best match neutron beam performance with scattering instrument needs. The burnup that comes with use changes the performance of the moderators until they no longer server their intended purpose. The reasonable desire to maximize the IRP lifetime means that the moderator performance at the Beginning Of Life (BOL) is significantly “over poisoned” and different from the performance at moderator End Of Life (EOL). Upon installation of the second IRP article, IRP-2, the SNS Neutronics team characterized the performance of the neutron beamlines in order to assess the differences between them, primarily by comparing the EOL performance of IRP-1 to the BOL performance of IRP-2. While IRP-2 was largely similar to IRP-1 in its conceptual design, there were some differences in the specific design of IRP-2 to support enhanced manufacturability, and the change from IPR-1 to IRP-2 coincided with the replacement of the light water in the IRP cooling loop with heavy water, as had been intended in the SNS design but not implemented during construction because of heavy water availability.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Seismicity and plate tectonics in south central Alaska

Hypocenter distribution shows that the Benioff zone associated with the Aleutian arc terminates in interior Alaska some 75 km north of the Denali fault. There appears to be a break in the subducting Pacific plate in the Yentna River-Prince William Sound area which separates two seismically independent blocks, similar to the segmented structure reported for the central Aleutian arc.

Van Wormer, J. D.↗

Improved ultrasonic standard reference blocks

A program to improve the quality, reproducibility and reliability of nondestructive testing through the development of improved ASTM-type ultrasonic reference standards is described. Reference blocks of aluminum, steel, and titanium alloys are to be considered. Equipment representing the state-of-the-art in laboratory and field ultrasonic equipment was obtained and evaluated. RF and spectral data on ten sets of ultrasonic reference blocks have been taken as part of a task to quantify the variability in response from nominally identical blocks. Techniques for residual stress, preferred orientation, and micro-structural measurements were refined and are applied to a reference block rejected by the manufacturer during fabrication in order to evaluate the effect of metallurgical condition on block response. New fabrication techniques for reference blocks are discussed and ASTM activities are summarized.

Eitzen, D. G.↗

User's manual for FRAC3D: Supplement to report on stress analysis for structures with surface cracks

The FRAC3D computer program, designed for use in analyzing stresses in structures (including plates, bars, or blocks) which may contain part-circular surface cracks or embedded circular cracks is described. Instructions are provided for preparing input, including that for the supporting programs LATTICE and MATSOL as well as for FRAC3D. The course of a substantial illustrative calculation is shown with both input and output. The formulas underlying the calculations are summarized and related to the subroutines in which they are used. Many issues of strategy in using this program for analysing stresses around surface cracks are elucidated.

Bell, J. C.↗

Prospects of a mathematical theory of human behavior in complex man-machine systems tasks

A hierarchy of human activities is derived by analyzing automobile driving in general terms. A structural description leads to a block diagram and a time-sharing computer analogy. The range of applicability of existing mathematical models is considered with respect to the hierarchy of human activities in actual complex tasks. Other mathematical tools so far not often applied to man machine systems are also discussed. The mathematical descriptions at least briefly considered here include utility, estimation, control, queueing, and fuzzy set theory as well as artificial intelligence techniques. Some thoughts are given as to how these methods might be integrated and how further work might be pursued.

Johannsen, G.↗

Mathematical concepts for modeling human behavior in complex man-machine systems

Many human behavior (e.g., manual control) models have been found to be inadequate for describing processes in certain real complex man-machine systems. An attempt is made to find a way to overcome this problem by examining the range of applicability of existing mathematical models with respect to the hierarchy of human activities in real complex tasks. Automobile driving is chosen as a baseline scenario, and a hierarchy of human activities is derived by analyzing this task in general terms. A structural description leads to a block diagram and a time-sharing computer analogy.

Johannsen, G.↗

Composite beam builder

The building block approach to large space structures is discussed, and the progress made in constructing aluminum beams is noted. It is pointed out that composites will also be required in space structures because they provide minimal distortion characteristics during thermal transients. A composite beam builder currently under development is discussed, with attention given to cap forming and the fastening of cross-braces. The various composite materials being considered are listed, along with certain of their properties. The need to develop continuous forming stock up to 300 m long is stressed.

Poveromo, L. M.↗

Supercomputer optimizations for stochastic optimal control applications

Supercomputer optimizations for a computational method of solving stochastic, multibody, dynamic programming problems are presented. The computational method is valid for a general class of optimal control problems that are nonlinear, multibody dynamical systems, perturbed by general Markov noise in continuous time, i.e., nonsmooth Gaussian as well as jump Poisson random white noise. Optimization techniques for vector multiprocessors or vectorizing supercomputers include advanced data structures, loop restructuring, loop collapsing, blocking, and compiler directives. These advanced computing techniques and superconducting hardware help alleviate Bellman's curse of dimensionality in dynamic programming computations, by permitting the solution of large multibody problems. Possible applications include lumped flight dynamics models for uncertain environments, such as large scale and background random aerospace fluctuations.

Chung, Siu-Leung↗

A generalized patched-grid algorithm with application to the F-18 forebody with actuated control strake

Analysis of complex configurations using structured grids virtually demands multiple blocks of grids. To facilitate calculations involving multiple blocks, a geneal grid-block patching algorithm based on generalized coordinate inerpolation has been developed. The computational grid may contain as many arbirarily shaped blocks as required to make the grid generation problem tractable and to accurately model the fow features. Results are presented for several test cases as well as for the F-18 forebody control strake. The methodology developed has application to overlapped or embedded grids.

Biedron, R. T.↗