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Core packing of well-defined x-ray and NMR structures is the same

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arXiv 2022年

作者： Grigas, Alex T. Liu, Zhuoyi Regan, Lynne O’Hern, Corey S. Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Institute of Quantitative Biology Biochemistry and Biotechnology Centre for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh United Kingdom Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

Numerous studies have investigated the differences and similarities between protein structures determined by solution NMR spectroscopy and those determined by x-ray crystallography. A fundamental question is whether any observed differences are due to differing methodologies, or to differences in the behavior of proteins in solution versus in the crystalline state. Here, we compare the properties of the hydrophobic cores of high-resolution protein crystal structures and those in NMR structures, determined using increasing numbers and types of restraints. Prior studies have reported that many NMR structures have denser cores compared to those of high-resolution x-ray crystal structures. Our current work investigates this result in more detail, and finds that these NMR structures tend to violate basic features of protein stereochemistry, such as small non-bonded atomic overlaps and few Ramachandran and side chain dihedral angle outliers. We find that NMR structures solved with more restraints, and which do not significantly violate stereochemistry, have hydrophobic cores that have a similar size and packing fraction as their counterparts determined by x-ray crystallography at high-resolution. These results lead us to conclude that, at least regarding the core packing properties, high-quality structures determined by NMR and x-ray crystallography are the same, and the differences reported earlier are most likely a consequence of methodology, rather than fundamental differences between the protein in the two different environments. Significance: Dense packing of hydrophobic residues is key to protein structure and stability. Previously, it has been noted that structures solved by NMR spectroscopy have denser cores than x-ray crystal structures. Here, we calculate the core size and packing fraction of NMR structures with experimental restraints in the PDB. Their cores are typically smaller, but denser. However, NMR structures with accurate stereochemistry possess core pa

关键词： X ray crystallography

Ultra-Cold Cryogenic TEM Sample Holder with Liquid Helium and High Stability

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Microscopy and Microanalysis 2024年第SUPPLEMENT_1期30卷

作者： Gates, Maya Rennich, Emily Sung, Suk Hyun Agarwal, Nishkarsh Kerns, Robert Hovden, Robert Baggari, Ismail El Department of Mechanical Engineerin University of Michigan Ann Arbor MI USA Rowland Institute at Harvard University Cambridge MA USA Department of Materials Science & Engineering University of Michigan Ann Arbor MI USA Michigan Center for Materials Characterization University of Michigan Ann Arbor MI USA Applied Physics Program University of Michigan Ann Arbor MI USA

Towards realistic simulations of human cough: effect of droplet emission duration and spread angle

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arXiv 2022年

作者： Li, Mogeng Chong, Kai Leong Ng, Chong Shen Bahl, Prateek de Silva, Charitha M. Verzicco, Roberto Doolan, Con MacIntyre, C. Raina Lohse, Detlef Physics of Fluids Group Max Planck Center for Complex Fluid Dynamics J. M. Burgers Center for Fluid Dynamics and MESA+ Research Institute Department of Science and Technology University of Twente Enschede7500AE Netherlands Max Planck Institute for Dynamics and Self-Organisation Göttingen37077 Germany Shanghai Key Laboratory of Mechanics in Energy Engineering Shanghai Institute of Applied Mathematics and Mechanics School of Mechanics and Engineering Science Shanghai University Shanghai200072 China School of Mechanical and Manufacturing Engineering UNSW Sydney KensingtonNSW2052 Australia Dipartimento di Ingegneria Industriale University of Rome 'Tor Vergata' Roma00133 Italy Gran Sasso Science Institute Viale F. Crispi L'Aquila7 67100 Italy Biosecurity Program The Kirby Institute UNSW Sydney KensingtonNSW2052 Australia College of Public Service & Community Solutions College of Health Solutions Arizona State University PhoenixAZ United States

Human respiratory events, such as coughing and sneezing, play an important role in the host-to-host airborne transmission of diseases. Thus, there has been a substantial effort in understanding these processes: various analytical or numerical models have been developed to describe them, but their validity has not been fully assessed due to the difficulty of a direct comparison with real human exhalations. In this study, we report a unique comparison between datasets that have both detailed measurements of a real human cough using spirometer and particle tracking velocimetry, and direct numerical simulation at similar conditions. By examining the experimental data, we find that the injection velocity at the mouth is not uni-directional. Instead, the droplets are injected into various directions, with their trajectories forming a cone shape in space. Furthermore, we find that the period of droplet emissions is much shorter than that of the cough: experimental results indicate that the droplets with an initial diameter 10µm are emitted within the first 0.05 s, whereas the cough duration is closer to 1 s. These two features (the spread in the direction of injection velocity and the short duration of droplet emission) are incorporated into our direct numerical simulation, leading to an improved agreement with the experimental measurements. Thus, to have accurate representations of human expulsions in respiratory models, it is imperative to include parametrisation of these two features. © 2022, CC BY.

关键词： COVID-19

The mesoscale order of nacreous pearls

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arXiv 2021年

作者： Gim, Jiseok Koch, Alden Otter, Laura M. Savitzky, Benjamin H. Erland, Sveinung Estroff, Lara A. Jacob, Dorrit E. Hovden, Robert Department of Materials Science & Engineering University of Michigan Ann ArborMI48109 United States Department of Biomedical Engineering University of Michigan Ann ArborMI48109 United States Research School of Earth Sciences Australian National University CanberraACT2600 Australia National Center for Electron Microscopy Molecular Foundry Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Department of Maritime Studies Western Norway University of Applied Sciences Haugesund5528 Norway Department of Materials Science and Engineering Cornell University IthacaNY14853 United States Kavli Institute at Cornell for Nanoscale Science Cornell University IthacaNY14853 United States Applied Physics Program University of Michigan Ann ArborMI48109 United States

A pearl's distinguished beauty and toughness are attributable to the periodic stacking of aragonite tablets known as nacre. Nacre has naturally occurring mesoscale periodicity that remarkably arises in the absence of discrete translational symmetry. Gleaning the inspiring biomineral design of a pearl requires quantifying its structural coherence and understanding the stochastic processes that influence formation. By characterizing the entire structure of pearls (∼3 mm) in a cross-section at high resolution, we show that nacre has medium-range mesoscale periodicity. Self-correcting growth mechanisms actively remedy disorder and topological defects of the tablets and act as a countervailing process to longrange disorder. Nacre has a correlation length of roughly 16 tablets (∼5.5 μm) despite persistent fluctuations and topological defects. For longer distances (>25 tablets, ∼8.5 μm), the frequency spectrum of nacre tablets follows f-1.5behavior, suggesting that growth is coupled to external stochastic processes-a universality found across disparate natural phenomena, which now includes pearls. © 2021, CC BY.

关键词： Gems

Linear Aging Behavior at Short Timescales in Nanoscale Contacts

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Physical Review Letters 2020年第2期124卷 026801-026801页

作者： Kaiwen Tian Zhuohan Li Yun Liu Nitya N. Gosvami David L. Goldsby Izabela Szlufarska Robert W. Carpick Department of Physics and Astronomy University of Pennsylvania Philadelphia Pennsylvania 19104 USA Department of Materials Science and Engineering University of Wisconsin-Madison Madison Wisconsin 53706 USA Department of Chemistry and Chemical Biology Harvard University Cambridge Massachusetts 02138 USA Department of Mechanical Engineering and Applied Mechanics University of Pennsylvania Philadelphia Pennsylvania 19104 USA Department of Earth and Environmental Science University of Pennsylvania Philadelphia Pennsylvania 19104 USA

Nanoscale silica-silica contacts were recently found to exhibit logarithmic aging for times ranging from 0.1 to 100 s, consistent with the macroscopic rate and state friction laws and several other aging processes. Nanoscale aging in this system is attributed to progressive formation of interfacial siloxane bonds between surface silanol groups. However, understanding or even data for contact behavior for aging times <0.1 s, before the onset of logarithmic aging, is limited. Using a combination of atomic force microscopy experiments and kinetic Monte Carlo simulations, we find that aging is nearly linear with aging time at short timescales between ∼ 5 and 90 ms. We demonstrate that aging at these timescales requires the existence of a particular range of reaction energy barriers for interfacial bonding. Specifically, linear aging behavior consistent with experiments requires a narrow peak close to the upper bound of this range of barriers. These new insights into the reaction kinetics of interfacial bonding in nanoscale aging advance the development of physically based rate and state friction laws for nanoscale contacts.

关键词： Aging Chemical bonding Friction Surface & interfacial phenomena Tribology Atomic force microscopy Monte Carlo methods

Spectral evidence for unidirectional charge density wave in detwinned BaNi2As2

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Physical Review B 2023年第8期108卷 L081104-L081104页

作者： Yucheng Guo Mason Klemm Ji Seop Oh Yaofeng Xie Bing-Hua Lei Luca Moreschini Cheng Chen Ziqin Yue Sergey Gorovikov Tor Pedersen Matteo Michiardi Sergey Zhdanovich Andrea Damascelli Jonathan Denlinger Makoto Hashimoto Donghui Lu Chris Jozwiak Aaron Bostwick Eli Rotenberg Sung-Kwan Mo Rob G. Moore Junichiro Kono Robert J. Birgeneau David J. Singh Pengcheng Dai Ming Yi Department of Physics and Astronomy Rice University Houston Texas 77005 USA Advanced Light Source Lawrence Berkeley National Laboratory Berkeley California 94720 USA Department of Physics University of California Berkeley California 94720 USA Department of Physics and Astronomy University of Missouri Columbia Missouri 65211 USA Materials Science Division Lawrence Berkeley National Laboratory Berkeley California 94720 USA Department of Physics University of Oxford Oxford OX1 3PU United Kingdom Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston Texas 77005 USA Canadian Light Source Inc. 44 Innovation Boulevard Saskatoon SK S7N 2V3 Canada Department of Physics and Astronomy University of British Columbia Vancouver British Columbia V6T 1Z1 Canada Quantum Matter Institute University of British Columbia Vancouver British Columbia V6T 1Z4 Canada Max Planck Institute for Chemical Physics of Solids Nöthnitzer Straße 40 01187 Dresden Germany Stanford Synchrotron Radiation Lightsource SLAC National Accelerator Laboratory Menlo Park California 94025 USA Materials Science and Technology Division Oak Ridge National Laboratory Oak Ridge Tennessee 37831 USA Department of Electrical and Computer Engineering Rice University Houston Texas 77005 USA Smalley-Curl Institute Rice University Houston Texas 77005 USA Department of Materials Science and NanoEngineering Rice University Houston Texas 77005 USA Department of Chemistry University of Missouri Columbia Missouri 65211 USA

In the iron-based superconductors, unconventional superconductivity emerges in proximity to intertwined electronic orders consisting of an electronic nematic order and a spin density wave (SDW). Recently, BaNi2As2, like its well-known iron-based analog BaFe2As2, has been discovered to host a symmetry-breaking structural transition but coupled to a unidirectional charge density wave (CDW) instead of SDW, providing a novel platform to study intertwined orders. Here, through a systematic angle-resolved photoemission spectroscopy study combined with a detwinning B1g uniaxial strain, we identify distinct spectral evidence of band evolution due to the structural transition as well as CDW-induced band folding. In contrast to the nematicity and spin density wave in BaFe2As2, the structural and CDW order parameters in BaNi2As2 are observed to be strongly coupled and do not separate in the presence of uniaxial strain. Furthermore, no nematic band splitting is resolved above the structural transition. Our measurements point to a likely lattice origin of the CDW order in BaNi2As2.

关键词： Charge density waves Nematic phase transition Iron-based superconductors Angle-resolved photoemission spectroscopy

Kinetically Limited Growth of Dendritic Tin Oxide Thin Films: a Machine Learning Study beyond the Structure Zone Diagram

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Advanced science 2025年 e04627页

作者： Music, Denis Xiao, Xuelian Naser, Rami Chang, Keke Sadowski, Grzegorz Olsson, Pär A. T. Department of Materials Science and Applied Mathematics Malmö University MalmöSE-205 06 Sweden Biofilms Research Center for Biointerfaces Malmö University MalmöSE-205 06 Sweden State Key Laboratory of Advanced Marine Materials Ningbo Institute of Materials Technology and Engineering Chinese Academy of Sciences Ningbo315201 China Division of Mechanics Materials and Component Design Lund University P.O. Box 118 LundSE-221 00 Sweden

Even after fifty years since its introduction, the empirical Thornton's structure zone diagram remains a valuable tool for predicting thin film microstructure. This diagram is essential for understanding the correlation between synthesis, composition, structure, and physical properties in emerging applications. In this work, we critically appraise this diagram by examining Sn─O thin films grown at room temperature using reactive magnetron sputtering. Based on transmission electron microscopy, Sn0.6O0.4 thin films form dendrites featuring nanosized Sn and SnO grains, rather than columns, which are not captured by the structure zone diagram. Using density functional theory and machine learning, we constructed a model to explain this unusual microstructure on the atomic scale. Kinetically limited surface diffusion yields SnO islands on Sn(001), which constitute the initial stage of dendrite formation. This study provides the potential to devise models for thin film microstructure evolution, enhancing performance in advanced applications, such as green energy generation and storage. © 2025 The Author(s). Advanced science published by Wiley-VCH GmbH.

关键词： Nanocrystalline materials

Universal mechanical response of metallic glasses during strain-rate-dependent uniaxial compression

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arXiv 2022年

作者： Jin, Weiwei Datye, Amit Schwarz, Udo D. Shattuck, Mark D. O'Hern, Corey S. Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Chemical and Environmental Engineering Yale University New HavenCT06520 United States Benjamin Levich Institute Physics Department The City College of New York New YorkNY10031 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States

Experimental data on the compressive strength σmax versus strain rate Ε eng for metallic glasses undergoing uniaxial compression shows significantly different behavior for different alloys. For some metallic glasses, σmax decreases with increasing Ε eng, for others, σmax increases with increasing Ε eng, and for others σmax versus Ε eng is nonmonotonic. Using numerical simulations of metallic glasses undergoing uniaxial compression at nonzero strain rate and temperature, we show that they obey a universal relation for the compressive strength versus temperature, which determines their mechanical response. At low Ε eng, increasing strain rate leads to increases in temperature and decreases in σmax∗, whereas at high Ε eng, increasing strain rate leads to decreases in temperature and increases in σmax∗. This non-monotonic behavior of σmax∗ versus temperature causes the nonmonotonic behavior of σmax∗ versus Ε eng. Variations in the internal dissipation change the characteristic strain rate at which the nonmonotonic behavior occurs. These results are general for a wide range of metallic glasses with different atomic interactions, damping coefficients, and chemical compositions. © 2022, CC BY.

关键词： Strain rate

Field-driven metamorphoses of isolated skyrmions within the conical state of cubic helimagnets

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Physical Review B 2021年第6期104卷 064432-064432页

作者： Andrey O. Leonov C. Pappas Ivan I. Smalyukh Department of Chemistry Faculty of Science Hiroshima University Kagamiyama Higashi Hiroshima Hiroshima 739-8526 Japan Chirality Research Center Hiroshima University Higashi Hiroshima Hiroshima 739-8526 Japan IFW Dresden Postfach 270016 D-01171 Dresden Germany Faculty of Applied Sciences Delft University of Technology Mekelweg 15 2629JB Delft The Netherlands Soft Materials Research Center and Materials Science and Engineering Program University of Colorado Boulder Colorado 80309 USA Department of Physics and Department of Electrical Computer and Energy Engineering University of Colorado Boulder Colorado 80309 USA Renewable and Sustainable Energy Institute National Renewable Energy Laboratory and University of Colorado Boulder Colorado 80309 USA

Topologically stable field configurations appear in many fields of physics, from elementary particles to condensed matter and cosmology. Deep physical relations and common physical features of a large variety of very different solitonic states in these systems arise from the mathematical similarity of phenomenological equations. During the last decade, chiral liquid crystals and chiral magnets took on the role of model objects for the experimental investigation of topological solitons and the understanding of their nonsingular field configurations. This is directly related to the discovery of particle-like chiral skyrmions, which are also considered as promising ingredients for technological applications. Here we introduce a paradigm of facile skyrmionic networks with mutually orthogonal orientations of constituent isolated skyrmions. On the one hand, such networks are envisioned as a novel concept of spintronic devices based, e.g., on gapless skyrmion motion along each other, and are presumably responsible for precursor phenomena near the ordering temperatures of bulk cubic helimagnets. In particular, we demonstrate an interconversion between mutually orthogonal skyrmions: horizontal skyrmions may swirl into an intermediate spring-like state and subsequently squeeze into vertical skyrmions with both polarities. On the other hand, skyrmion tubes are considered as building blocks for particle-like states with more involved internal structure. A family of target-skyrmions, which includes a so far overlooked type with a multiple topological charge, is formed owing to the tendency to minimize the interaction energy between vertical and horizontal skyrmions. The conical phase serves as a suitable background for considered skyrmion evolution. It substantializes the attracting skyrmion-skyrmion interaction in the skyrmionic networks, shapes their internal structure, and guides the nucleation processes. Alternatively, intricate textural changes of isolated skyrmions result

关键词： Skyrmions Chiral magnets Cholesteric liquid crystals Helimagnets