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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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Green biomaterials: fundamental principles

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Green biomaterials 2023年第1期1卷

作者： Navid Rabiee Mehmet R. Dokmeci Ali Zarrabi Pooyan Makvandi Mohammad Reza Saeb Hassan Karimi-Maleh Shima Jafarzadeh Ceren Karaman Yusuke Yamauchi Majid Ebrahimi Warkiani Sidi A. Bencherif Geeta Mehta Miharu Eguchi Ajeet Kaushik Mohammad-Ali Shahbazi Ana Cláudia Paiva-Santos Jacek Ryl Eder C. Lima Michael R. Hamblin Rajender S. Varma YunSuk Huh A. T. Ezhil Vilian Piyush Kumar Gupta Sandeep Kumar Lakhera Kavindra Kumar Kesari Yu-Ting Liu Mohammadreza Tahriri Ganji Seeta Rama Raju Mohsen Adeli Ali Mohammadi Jianglin Wang Mohd Zahid Ansari Tejraj Aminabhavi Houman Savoji Gautam Sethi Tomasz Bączek Agata Kot-Wasik Marcela Elisabeth Penoff Abdorreza Mohammadi Nafchi Justyna Kucinska-Lipka Masoumeh Zargar Mohsen Asadnia Amir Reza Aref Moein Safarkhani Milad Ashrafizadeh Reddicherla Umapathi Amir Ghasemi Milica Radisic a Centre for Molecular Medicine and Innovative Therapeutics Murdoch University Perth WA Australiab School of Engineering Macquarie University Sydney New South Wales Australia c Terasaki Institute for Biomedical Innovation (TIBI) Los Angeles CA90024 USA d Department of Biomedical Engineering Faculty of Engineering and Natural Sciences Istinye University Sariyer Istanbul Turkey e The Quzhou Affiliated Hospital of Wenzhou Medical University Quzhou People’s Hospital Zhejiang Quzhou Chinaf School of Engineering Institute for Bioengineering The University of Edinburgh Edinburgh United Kingdom g Department of Polymer Technology Faculty of Chemistry Gdańsk University of Technology Gdańsk Poland h School of Resources and Environment University of Electronic Science and Technology of China 611731 Xiyuan Ave Chengdu P. R. Chinai School of Engineering Lebanese American University Byblos Lebanon j School of Engineering Edith Cowan University Joondalup WA Australia k Department of Electricity and Energy Akdeniz University Antalya Turkey l Australian Institute for Bioengineering and Nanotechnology (AIBN) and School of Chemical Engineering The University of Queensland Brisbane QLD Australiam Department of Materials Process Engineering Graduate School of Engineering Nagoya University Nagoya Japan n School of Biomedical Engineering University of Technology Sydney Sydney NSW Australiao Faculty of Science Institute for Biomedical Materials and Devices (IBMD) University of Technology Sydney Sydney NSW Australia p Chemical Engineering Department Northeastern University Boston MA USAq Department of Bioengineering Northeastern University Boston MA USAr Harvard John A. Paulson School of Engineering and Applied Sciences Harvard University Cambridge MA USA s Department of Biomedical Engineering University of Michigan Ann Arbor MI USAt Department of Materials Science and Engineering University of Michigan Ann Arbor MI USAu Macromolecular Science and Engineering

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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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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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Effect of natural rubber latex adhesive content on the physical and mechanical properties of agriboard from cassava stem wastes

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AIP Conference Proceedings 2022年第1期2563卷 040005页

作者： Nana Aprilliana Wahyu Hidayat Sandi Asmara Muhammad Adly Rahandi Lubis Samsul Bakri Sri Hidayati Graduate Program of Environmental Science Universitas Lampung Jl. Sumantri Brojonegoro 1 Bandar Lampung 35145 Lampung Indonesia Department of Forestry Faculty of Agriculture University of Lampung. Jl. Sumantri Brojonegoro 1 Bandar Lampung 35145 Lampung Indonesia Department of Agricultural Engineering Faculty of Agriculture University of Lampung Jl. Sumantri Brojonegoro 1 Bandar Lampung 35145 Lampung Indonesia Research Center for Biomaterials Indonesian Institute of Sciences (LIPI). Jl. Raya Bogor Km. 46 Cibinong Bogor 16911 West Java Indonesia Department of Agricultural Product Technology Faculty of Agriculture University of Lampung Jl. Sumantri Brojonegoro 1 Bandar Lampung 35145 Lampung Indonesia

Indonesia is one of the largest cassava producers globally, where the cassava wastes have not been optimally utilized yet. Cassava stems are lignocellulosic materials that are potential as raw materials for composite boards. This study aims to determine the effect of the adhesive content of Natural Rubber Latex (NRL) adhesive on the physical and mechanical properties of particleboard from the waste of cassava stems (agriboard). The NRL-based adhesives were formulated from natural rubber, poly(vinyl) alcohol, and isocyanate. The levels of NRL adhesive used were 10%, 15%, and 20%. The agriboard panels were prepared with a size of 400 mm×400 mm×10 mm and a target density of 0.7 g/cm3. The board was hot-pressed at 60°C under 10 MPa of pressure for 30 minutes. Evaluation of physical and mechanical properties was done according to JIS 5908-2003 standard. The results showed that the density of agriboard ranged from 0.65–0.74 g/cm3, and the moisture content was around 4.51–5.34%. Water absorption and thickness swelling of agriboard panel ranged from 61.84–70.84% and 23.67–28.77%, respectively. The results revealed that the dimensional stability of agriboard increased with the higher adhesive content, indicating that the urethane linkages produced from the reaction between –NCO of isocyanate and –OH of cassava stems enhanced the adhesion strength of the panel. The MOE and MOR values of agriboard were in the range of 229.20-331.38 MPa and 2.49-3.13 MPa, respectively. The mechanical properties of the panel also increased with higher adhesive content, and the optimum result was obtained by using 20% of adhesive content. In addition, the NRL-bonded panel did not emit formaldehyde, as the panel did not bond with formaldehyde-based adhesives. The results showed that cassava stems and NRL adhesive could be used as an alternative composite product that is renewable and environmentally friendly, particularly for non-structural and interior applications. Keywords: cassava stem, compos

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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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