Effects of thermal annealing on localization and strain in core/multishell GaAs/GaNAs/GaAs nanowires

Balagula, R M; Jansson, Mattias; Yukimune, Mitsuki; Stehr, Jan Eric; Ishikawa, Fumitaro; Chen, Weimin; Buyanova, Irina

doi:10.1038/s41598-020-64958-6

Cited by 10 publications

(4 citation statements)

References 60 publications

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“…One can also anneal organic/inorganic semiconductors via rearranging molecules, polymer chain segments, or entire polymer chains into active layer films. Optimizing the annealing temperature and time can either dramatically increase the crystal size from the sub-micrometer scale to several micrometers, or yield different crystals (3–5).…”

Section: Introductionmentioning

confidence: 99%

Annealing synchronizes the 70S ribosome into a minimum-energy conformation

Chu

et al. 2021

Preprint

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Researchers commonly anneal metals, alloys, and semiconductors to repair defects and improve microstructures via recrystallization. Theoretical studies indicate simulated annealing on biological macromolecules helps predict the final structures with minimum free energy. Experimental validation of this homogenizing effect and further exploration of its applications are fascinating scientific questions that remain elusive. Here, we chose the apo-state 70S ribosome from Escherichia coli as a model, wherein the 30S subunit undergoes a thermally driven inter-subunit rotation and exhibits substantial structural flexibility as well as distinct free energy. We experimentally demonstrate that annealing at a fast cooling rate enhances the 70S ribosome homogeneity and improves local resolution on the 30S subunit. After annealing, the 70S ribosome is in a nonrotated state with respect to corresponding intermediate structures in unannealed or heated ribosomes, and exhibits a minimum energy in the free energy landscape. One can readily crystallize these minimum-energy ribosomes, which have great potential for synchronizing proteins on a single-molecule level. Our experimental results are consistent with theoretical analysis on the temperature-dependent Boltzmann distribution, and offer a facile yet robust approach to enhance protein stability, which is ideal for high-resolution cryogenic electron microscopy. Beyond structure determination, annealing can be extended to study protein folding and explore conformational and energy landscape.

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Section: Introductionmentioning

confidence: 99%

Annealing synchronizes the 70S ribosome into a minimum-energy conformation

Chu

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…One can also anneal organic/inorganic semiconductors via rearranging molecules, polymer chain segments, or entire polymer chains into active layer films. Optimizing the annealing temperature and time can either dramatically increase the crystal size from the submicrometer scale to several micrometers or yield different crystals ( 3 – 5 ).…”

mentioning

confidence: 99%

Annealing synchronizes the 70 S ribosome into a minimum-energy conformation

Chu

Liu

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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Researchers commonly anneal metals, alloys, and semiconductors to repair defects and improve microstructures via recrystallization. Theoretical studies indicate that simulated annealing on biological macromolecules helps predict the final structures with minimum free energy. Experimental validation of this homogenizing effect and further exploration of its applications are fascinating scientific questions that remain elusive. Here, we chose the apo-state 70S ribosome from Escherichia coli as a model, wherein the 30S subunit undergoes a thermally driven intersubunit rotation and exhibits substantial structural flexibility as well as distinct free energy. We experimentally demonstrate that annealing at a fast cooling rate enhances the 70S ribosome homogeneity and improves local resolution on the 30S subunit. After annealing, the 70S ribosome is in a nonrotated state with respect to corresponding intermediate structures in unannealed or heated ribosomes. Manifold-based analysis further indicates that the annealed 70S ribosome takes a narrow conformational distribution and exhibits a minimum-energy state in the free-energy landscape. Our experimental results offer a facile yet robust approach to enhance protein stability, which is ideal for high-resolution cryogenic electron microscopy. Beyond structure determination, annealing shows great potential for synchronizing proteins on a single-molecule level and can be extended to study protein folding and explore conformational and energy landscapes.

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“…Nanowireswith several shells [134]. From equations (3.2), it may be shown that the dominant strain component is the uniaxial component along the nanowire axis [133].…”

mentioning

confidence: 99%

Magnetooptical properties of dilute nitride nanowires

Jansson

2020

Linköping Studies in Science and Technology. Dissertations

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Nanotrådar av utspädda nitrider för framtidens optoelektronikNanotrådar gjorda av utspädda nitrider är ett nytt och spännande material som kan bli användbart i framtidens optoelektronik. Sådana nanotrådar kan nämligen lysa och absorbera ljus mycket effektivt, och i många olika färger. De ger dessutom upphov till exotiska nanostrukturer, så kallade kvantprickar, som spontant bildas i nanotrådarna. PrefaceThis thesis summarizes the outcome of Mattias Jansson's doctoral studies, conducted between 2015-2020 at the Department of Physics, Chemistry and Biology at Linköping University. The thesis is divided into two parts: The first part contains an introduction to the research field and of the experimental techniques used in this work. The second part contains the main research results, presented in seven scientific papers. ix x Preface AcknowledgementsFirst and foremost, to Irina Buyanova and Weimin Chen, thank you for hiring me as a PhD student in your research group. I cannot emphasize enough how lucky I feel to have ended up here. Thank you for pushing me to become a better experimentalist and researcher.To Jan Stehr, thank you for your guidance, support and inspiration, both inside and outside of the lab. And, of course, thank you for teaching me how to perform ODRM measurements (in 120 easy steps). I want to thank all past and present colleagues in the Functional Electronic Materials group for the support and inspiration you have provided. Especially, I wish to thank Yuttapoom Puttisong, Shula Chen, Stanislav Filippov and Yuqing Huang, for your support and guidance in the lab from day one, and for the inspiration you have given me in how to be a good researcher. Stanislav, thank you for introducing me to the µPL technique and the dilute nitride nanowires. To Roman Balagula, thank you for the fun and interesting times in the lab and during the office discussions, and for your helpful tips regarding the measurements. Thank you also for sharing the mixed excitement and frustration over the polarization measurements. To Bin Zhang, thank you for the collaborations in measuring the GaBiAs nanowires, and for your often difficult but always interesting questions and discussions. Till Pontus Höjer, tack för de intressanta diskussionerna vi haft på labbet, och över lunchen. Förlåt för att jag klev på ditt prov.To Professors Fumitaro Ishikawa at Ehime University and Charles Tu at University of California, San Diego, I direct my deep thanks for providing such excellent samples. I want to thank Professor Anna Fontcuberta i Morral and Luca Francaviglia at EPFL, for your collaboration involving the CL measurements. I also want to thank Thomas Lingefelt for your technical assistance with the electron microscopes, and for teaching me how to use the SEM, and Justinas Palisaitis for your help with the TEM measurements.I want to thank Plamen Paskov for allowing me to use the photon correlation setup, and for having me as a lab assistant in your course, where I learned a lot. Till Martin Eriksson, tack för all ovärderlig hjälp du get...

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Effects of thermal annealing on localization and strain in core/multishell GaAs/GaNAs/GaAs nanowires

Cited by 10 publications

References 60 publications

Annealing synchronizes the 70S ribosome into a minimum-energy conformation

Annealing synchronizes the 70S ribosome into a minimum-energy conformation

Annealing synchronizes the 70 S ribosome into a minimum-energy conformation

Magnetooptical properties of dilute nitride nanowires

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