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Control of microswimmers by spiral nematic vortices: transition from individual to collective motion and contraction, expansion, and stable circulation of bacterial swirls

arXiv

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arXiv 2020年

作者： Koizumi, Runa Turiv, Taras Genkin, Mikhail M. Lastowski, Robert J. Yu, Hao Chaganava, Irakli Wei, Qi-Huo Aranson, Igor S. Lavrentovich, Oleg D. Advanced Materials and Liquid Crystal Institute Materials Science Graduate Program Kent State University KentOH44242 United States Cold Spring Harbor Laboratory 1 Bungtown Rd Cold Spring HarborNY11724 United States Department of Chemistry University of Scranton ScrantonPA18510 United States Institute of Cybernetics of Georgian Technical University TbilisiGA0186 United States Georgian State Teaching University of Physical Education and Sport TbilisiGA0162 United States Department of Physics Kent State University KentOH44242 United States Department of Biomedical Engineering Pennsylvania State University University ParkPA16802 United States

Active systems comprised of self-propelled units show fascinating transitions from Brownian-like dynamics to collective coherent motion. Swirling of swimming bacteria is a spectacular example. This study demonstrates that a nematic liquid crystal environment patterned as a spiral vortex controls individual-to-collective transition in bacterial swirls and defines whether they expand or shrink. In dilute dispersions, the bacteria swim along open spiral trajectories, following the pre-imposed molecular orientation. The trajectories are nonpolar. As their concentration exceeds some threshold, the bacteria condense into unipolar circular swirls resembling stable limit cycles. This collective circular motion is controlled by the spiral angle that defines the splay-to-bend ratio of the background director. Vortices with dominating splay shrink the swirls towards the center, while vortices with dominating bend expand them to the periphery. 45o spiraling vortices with splay-bend parity produce the most stable swirls. All the dynamic scenarios are explained by hydrodynamic interactions of bacteria mediated by the patterned passive nematic environment and by the coupling between the concentration and orientation. The acquired knowledge of how to control individual and collective motion of microswimmers by a nematic environment can help in the development of microscopic mechanical systems. Copyright © 2020, The Authors. All rights reserved.

关键词： Vortex flow

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Void distributions reveal structural link between jammed packings and protein cores

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Physical Review E 2019年第2期99卷 022416-022416页

作者： John D. Treado Zhe Mei Lynne Regan Corey S. O'Hern Department of Mechanical Engineering & Materials Science Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical & Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Chemistry Yale University New Haven Connecticut 06520 USA Department of Molecular Biophysics & Biochemistry Yale University New Haven Connecticut 06520 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA

Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction ϕ≈0.56, which is the same as dense, random packing of amino-acid-shaped particles. In this article, we compare the structural properties of protein cores and jammed packings of amino-acid-shaped particles in much greater depth by measuring their local and connected void regions. We find that the distributions of surface Voronoi cell volumes and local porosities obey similar statistics in both systems. We also measure the probability that accessible, connected void regions percolate as a function of the size of a spherical probe particle and show that both systems possess the same critical probe size. We measure the critical exponent τ that characterizes the size distribution of connected void clusters at the onset of percolation. We find that the cluster size statistics are similar for void percolation in packings of amino-acid-shaped particles and randomly placed spheres, but different from that for void percolation in jammed sphere packings. We propose that the connected void regions are a defining structural feature of proteins and can be used to differentiate experimentally observed proteins from decoy structures that are generated using computational protein design software. This work emphasizes that jammed packings of amino-acid-shaped particles can serve as structural and mechanical analogs of protein cores, and could therefore be useful in modeling the response of protein cores to cavity-expanding and -reducing mutations.

关键词： Jamming Protein structure Packing & jamming problems Proteins Crystal structures Finite-size scaling Molecular dynamics Percolation theory

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Liquid-EM goes viral - visualizing structure and dynamics

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Current opinion in structural biology 2022年 75卷 102426页

作者： Deborah F Kelly Liza-Anastasia DiCecco G M Jonaid William J Dearnaley Michael S Spilman Jennifer L Gray Madeline J Dressel-Dukes Department of Biomedical Engineering Pennsylvania State University University Park PA 16802 USA Center for Structural Oncology Pennsylvania State University University Park PA 16802 USA Materials Research Institute Pennsylvania State University University Park PA 16802 USA. Electronic address: Debkelly@psu.edu. Department of Materials Science and Engineering McMaster University Hamilton ON L8S 4L7 Canada. Electronic address: https://***/LizaDiCecco. Bioinformatics and Genomics Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park PA 16802 USA. Materials Research Institute Pennsylvania State University University Park PA 16802 USA. Electronic address: https://***/PennStateMRI. Direct Electron LP San Diego CA 92128 USA. Electronic address: https://***/DirectElectron. Materials Research Institute Pennsylvania State University University Park PA 16802 USA. Protochips Inc. Morrisville NC 27560 USA. Electronic address: https://***/Protochips.

Liquid-electron microscopy (EM), the room temperature correlate to cryo-EM, is an exciting new technique delivering real-time data of dynamic reactions in solution. Here, we explain how liquid-EM gained popularity in recent years by examining key experiments conducted on viral assemblies and host-pathogen interactions. We describe developing workflows for specimen preparation, data collection, and computing processes that led to the first high-resolution virus structures in a liquid environment. Equally important, we review why liquid-electron tomography may become the next big thing in biomedical research due to its ability to monitor live viruses entering cells within seconds. Taken together, we pose the idea that liquid-EM can serve as a dynamic complement to current cryo-EM methods, inspiring the "real-time revolution" in nanoscale imaging.

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Cover Feature: Quantum Mechanical Calculations for Biomass Valorization over Metal-Organic Frameworks (MOFs) (Chem. Asian J. 9/2021)

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Chemistry – An Asian Journal 2021年第9期16卷

作者： Jyun-Yi Yeh Shih-Cheng Li Celine H. Chen Prof. Kevin C.-W. Wu Prof. Yi-Pei Li International Graduate Program of Molecular Science and Technology (NTU-MST) National Taiwan University No. 1 Sec. 4 Roosevelt Road Taipei 10617 Taiwan Taiwan International Graduate Program (TIGP) Academia Sinica No. 128 Sec. 2 Academia Road Taipei 11529 Taiwan Department of Chemical Engineering National Taiwan University No. 1 Sec. 4 Roosevelt Road Taipei 10617 Taiwan School of Engineering Brown University 184 Hope St Providence RI 02912 United States Center of Atomic Initiative for New Materials National Taiwan University No. 1 Sec. 4 Roosevelt Road Taipei 10617 Taiwan

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Ionic oxidation in cathodic cage of titanium CP grade II

Ionic oxidation in cathodic cage of titanium CP grade II

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作者： Vitoriano, Jussier Oliveira Braz, Danilo Cavalcante Barbosa, Geovani Ferreira Araújo, Francisco Odolberto Alves, Clodomiro Post-Graduate Program in Materials Science and Engineering Universidade Federal Rural do Semi-Árido Brazil

Titanium oxides such as rutile and anatase, are materials that stand out for exhibiting properties that act in biomedical and photocatalytic applications, among others. It is extreme importance to idealize new techniques that produce such compounds, being indispensable the improvement of characterizations for these materials. For this purpose, titanium comercially pure (CP) grade II cylindrical samples were oxidized ionically using titanium cage electric shields, oxidized at 350 ° C in 3 and 8 hours. Through Grazing Incidence X-ray Diffraction (GIXRD) analysis, was observed on the surface of the treated samples the formation of a TiO2 film with the anatase, rutile and brookite phases, the latter phase cited being difficult to produce in conventional thermochemical treatments. All samples treated showed a significant increase in wettability using distilled water. The higer value was for the sample with a 8 hours treatment time, in which this condition presented phases with greater intensity in the analysis of GIXRD. © 2017 Universidade Federal de Sao Carlos. All rights reserved.

关键词： Titanium dioxide

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Tunneling spectroscopy of c-axis epitaxial cuprate junctions

arXiv

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arXiv 2020年

作者： Zhou, Panpan Chen, Liyang Sochnikov, Ilya Wu, Tsz Chun Foster, Matthew S. Bollinger, Anthony T. He, Xi Božović, Ivan Natelson, Douglas Department of Physics and Astronomy Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Department of Physics University of Connecticut StorrsCT06269 United States Brookhaven National Laboratory UptonNY11973-5000 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States

Atomically precise epitaxial structures are unique systems for tunneling spectroscopy that minimize extrinsic effects of disorder. We present a systematic tunneling spectroscopy study, over a broad doping, temperature, and bias range, in epitaxial c-axis La2−xSrxCuO4/La2CuO4/La2−xSrxCuO4 heterostructures. The behavior of these superconductor/insulator/superconductor (SIS) devices is unusual. Down to 20 mK there is complete suppression of c-axis Josephson critical current with a barrier of only 2 nm of La2CuO4, and the zero-bias conductance remains at 20-30% of the normal-state conductance, implying a substantial population of in-gap states. Tunneling spectra show greatly suppressed coherence peaks. As the temperature is raised, the superconducting gap fills in rather than closing at Tc. For all doping levels, the spectra show an inelastic tunneling feature at ∼ 80 meV, suppressed as T exceeds Tc. These nominally simple epitaxial cuprate junctions deviate markedly from expectations based on the standard Bardeen-Cooper-Schrieffer (BCS) theory. Copyright © 2020, The Authors. All rights reserved.

关键词： Copper compounds

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Skeletal Muscle Regeneration: Functional Skeletal Muscle Regeneration with Thermally Drawn Porous Fibers and Reprogrammed Muscle Progenitors for Volumetric Muscle Injury (Adv. Mater. 14/2021)

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Advanced materials 2021年第14期33卷

作者： Yoonhee Jin Dena Shahriari Eun Je Jeon Seongjun Park Yi Sun Choi Jonghyeok Back Hyungsuk Lee Polina Anikeeva Seung-Woo Cho Department of Biotechnology Yonsei University Seoul 03722 Republic of Korea Research Laboratory of Electronics Massachusetts Institute of Technology Cambridge MA 02139 USA McGovern Institute for Brain Research Cambridge MA 02139 USA Department of Biomaterials Science and Engineering Yonsei University Seoul 03722 Republic of Korea Department of Bio and Brain Engineering Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea KAIST Institute for Health Science and Technology Daejeon 34141 Republic of Korea School of Mechanical Engineering Yonsei University Seoul 03722 Republic of Korea Department of Materials Science and Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA Department of Brain and Cognitive Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA Center for Nanomedicine Institute for Basic Science (IBS) Seoul 03722 Republic of Korea Graduate Program of Nano Biomedical Engineering (NanoBME) Advanced Science Institute Yonsei University Seoul 03722 Republic of Korea

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Influence of MIG/MAG Welding Process on Mechanical and Pitting Corrosion Behaviors on the Super-Duplex Stainless Steel SAF 2507 Welded Joints

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materials sciences and Applications 2018年第2期9卷 228-245页

作者： Bruno Leonardy S. Lopes Samuel F. Rodrigues Eden S. Silva Gedeon S. Reis Waldemir dos P. Martins Juvenilson Costa Damascena Valdemar S. Leal Graduate Program in Materials Engineering Federal Institute of Education Science and Technology of Maranh&atilde o—IFMA S&atilde o Luís MA Brazil Engineering Coordination Universidade UNICEUMA S&atilde o Luís MA Brazil

The main objective of this research is to better understand the correlation between the constituent phases presented in the super-duplex steel SAF 2507 when it is under welding process by arc shielding gas MIG-MAG (Metal Inert Gas-Metal Active Gas). Conventional short circuit transfer and derivative STT (Surface Tension Transfer) using the 2594 welding wire as a filler metal and the effects on welding power in hardness, toughness and pitting corrosion are considered here. The results showed that the welding energy (Ew) changed the α/γ-phase’s balance and occasionally formed σ-phase in ferrite grain boundaries which led to changes in hardness, toughness and pitting corrosion resistance in molten zone (MZ), heat activated zone (HAZ) and metal base regions (MB). Furthermore, the increased amount of γ-phase improved the pitting corrosion resistance index (PRENγ) mainly in the MZ. This is due to decrease of α-phase fraction and formation of coarser grains, for higher welding energy. The toughness in the MZ decreased with less formation of γ-phase, coalescence of ferritic grains and localized formation of σ-phase, raising the hardness in the HAZ when the welding energy was lower.

关键词： Super-Duplex Steels Welding Toughness Pitting Corrosion Microhardness

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Tunable plasmonic ultrastrong coupling: Emulating dicke physics at room temperature

arXiv

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arXiv 2021年

作者： Yahiaoui, Riad Chase, Zizwe A. Kyaw, Chan Tay, Fuyang Baydin, Andrey Noe, G. Timothy Song, Junyeob Kono, Junichiro Agrawal, Amit Bamba, Motoaki Searles, Thomas A. Department of Physics and Astronomy Howard University WashingtonDC20059 United States Department of Electrical and Computer Engineering Rice University HoustonTX70005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Smalley-Curl Institute Rice University HoustonTX77005 United States Physical Measurement Laboratory National Institute of Standards and Technology GaithersburgMD20899 United States Department of Physics and Astronomy Rice University HoustonTX77005 United States Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States Maryland NanoCenter University of Maryland College ParkMD20742 United States The Hakubi Center for Advanced Research Kyoto University Kyoto606-8502 Japan Department of Physics I Kyoto University Kyoto606-8502 Japan Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States

A system of N two-level atoms cooperatively interacting with a photonic field can be described as a single giant atom coupled to the field with interaction strength ∝ √N. This enhancement, known as Dicke cooperativity in quantum optics, has recently become an indispensable element in quantum information technology based on strong light-matter coupling. Here, we extend the coupling beyond the standard light-matter interaction paradigm, emulating Dicke cooperativity in a terahertz metasurface with N meta-atoms. Cooperative enhancement manifested in the form of matter-matter coupling, through the hybridization of localized surface plasmon resonance in individual meta-atoms and surface lattice resonance due to the periodic array of the meta-atoms. By varying the lattice constant of the array, we observe a clear anticrossing behavior, a signature of strong coupling. Furthermore, through engineering of the capacitive split-gap in the meta-atoms, the coupling rate was cooperatively enhanced into the ultrastrong coupling regime by a factor of √N. This room-temperature technology serves as a convenient quantum emulator of the dynamics of a qubit with a giant dipole moment coherently driven by a single bosonic field. Copyright © 2021, The Authors. All rights reserved.

关键词： Atoms

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All-optical reconfigurable chiral meta-molecules

arXiv

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arXiv 2019年

作者： Lin, Linhan Lepeshov, Sergey Krasnok, Alex Jiang, Taizhi Peng, Xiaolei Korgel, Brian A. Alu, Andrea Zheng, Yuebing Department of Mechanical Engineering University of Texas at Austin AustinTX78712 United States Materials Science & Engineering Program Texas Materials Institute University of Texas at Austin AustinTX78712 United States ITMO University St. Petersburg197101 Russia Department of Electrical and Computer Engineering University of Texas at Austin AustinTX78712 United States Mc Ketta Department of Chemical Engineering University of Texas at Austin AustinTX78712 United States Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States Physics Program Graduate Center City University of New York NY10016 United States Department of Electrical Engineering City College of The City University New YorkNY10031 United States

Chirality is a ubiquitous phenomenon in the natural world. Many biomolecules without inversion symmetry such as amino acids and sugars are chiral molecules. Measuring and controlling molecular chirality at a high precision down to the atomic scale are highly desired in physics, chemistry, biology, and medicine, however, have remained challenging. Herein, we achieve all-optical reconfigurable chiral meta-molecules experimentally using metallic and dielectric colloidal particles as artificial atoms or building blocks to serve at least two purposes. One is that the on-demand meta-molecules with strongly enhanced optical chirality are well-suited as substrates for surface-enhanced chiroptical spectroscopy of chiral molecules and as active components in optofluidic and nanophotonic devices. The other is that the bottom-up-assembled colloidal meta-molecules provide microscopic models to better understand the origin of chirality in the actual atomic and molecular systems. Copyright © 2019, The Authors. All rights reserved.

关键词： Atoms

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