structural transitions
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2022 ◽  
Vol 211 ◽  
pp. 114502
Author(s):  
Tianjiao Lei ◽  
Mingjie Xu ◽  
Jungho Shin ◽  
Daniel S. Gianola ◽  
Timothy J. Rupert

2022 ◽  
Vol 64 (3) ◽  
pp. 313
Author(s):  
Д.А. Рыжкова ◽  
С.Л. Гафнер ◽  
Ю.Я. Гафнер

A comparative analysis of thermally induced structural transitions in silver nanoclusters, the number of atoms of which corresponded to the “magic” numbers of the icosahedral (Ih) structure with variation of their initial morphology, was carried out by the molecular dynamics method using the modified tight-binding potential TB-SMA. It is shown that, in the case of the initial fcc phase, the formation of the Ih modification, depending on the particle size, occurred either at the stage of preliminary thermal relaxation or during further heating. At the initial amorphous morphology, the nature of the structural transitions underwent significant changes. Thus, even in the case of Ag55 clusters, the icosahedral structure was formed only in 50-60% of the experiments performed. Based on the data obtained, it was concluded that to create a stable Ih structure, it is necessary to use the thermal cycling procedure.


Author(s):  
Дарья Антоновна Рыжкова ◽  
Светлана Леонидовна Гафнер ◽  
Юрий Яковлевич Гафнер

В статье методом молекулярной динамики с использованием модифицированного потенциала сильной связи TB-SMA (second moment approximation of tight-binding) проводится сравнительный анализ характера термически индуцированных структурных переходов в нанокластерах серебра, число атомов в которых соответствует «магическим» числам икосаэдрической структуры, при вариации их начальной морфологии. Показано, что в случае начальной ГЦК конфигурации формирование Ih модификации происходит либо на этапе предварительной термической релаксации, либо в ходе дальнейшего нагрева. При начальной аморфной морфологии характер структурных переходов претерпевает значительные изменения. Так, например, формирующаяся Ih модификация обладает большей стабильностью в области высоких температур и точка плавления нанокластеров смещается на величину более 100 К. Такой эффект обусловлен более плавным изменением удельной потенциальной энергии нанокластера в сравнении со случаем, когда устойчивая Ih конфигурация формируется при низких температурах. Полученные данные могут быть использованы при процессах создания нанокластеров серебра с требуемым внутренним строением. This article provides a comparative analysis of thermally induced structural transitions in silver nanoclusters with a change in their initial morphology. The study was executed by the molecular dynamics method using the modified TB-SMA (second moment approximation of tight-binding) tight binding potential. The number of atoms in nanoclusters corresponds to the icosahedral structure «magic» numbers. It is shown that for nanoclusters with the initial FCC configuration, the Ih modification is formed either at the stage of preliminary thermal relaxation or during further heating. For nanoclusters with an initial amorphous morphology, the nature of structural transitions undergoes significant changes. For example, the formed Ih modification is more stable at high temperatures and the melting point of nanoclusters shifts by more than 100 K. This effect is due to a smoother change in the specific potential energy of the nanocluster in comparison with the case when a stable Ih configuration is formed at low temperatures. The data obtained can be used in processes to create silver nanoclusters with the required internal structure.


2021 ◽  
Vol 528 ◽  
pp. 120607
Author(s):  
Łukasz Gondek ◽  
Stanisław M. Dubiel

2021 ◽  
pp. 163371
Author(s):  
Ruihong Li ◽  
Guangtao Liu ◽  
Qiang Jing ◽  
Xianyu Wang ◽  
Hongbo Wang ◽  
...  

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Sabrina Pospich ◽  
H Lee Sweeney ◽  
Anne Houdusse ◽  
Stefan Raunser

The molecular motor myosin undergoes a series of major structural transitions during its force-producing motor cycle. The underlying mechanism and its coupling to ATP hydrolysis and actin binding is only partially understood, mostly due to sparse structural data on actin-bound states of myosin. Here, we report 26 high-resolution cryo-EM structures of the actomyosin-V complex in the strong-ADP, rigor, and a previously unseen post-rigor transition state that binds the ATP analog AppNHp. The structures reveal a high flexibility of myosin in each state and provide valuable insights into the structural transitions of myosin-V upon ADP release and binding of AppNHp, as well as the actomyosin interface. In addition, they show how myosin is able to specifically alter the structure of F-actin.


Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6978
Author(s):  
Tingyi Wang ◽  
Hui Yan ◽  
Li Lv ◽  
Yingbiao Xu ◽  
Lingyu Zhang ◽  
...  

In this work, molecular dynamics simulations were performed to study the pH-induced structural transitions for a CTAB/p-toluic acid solution. Spherical and cylindrical micelles were obtained for aqueous surfactants at pH 2 and 7, respectively, which agrees well with the experimental observations. The structural properties of two different micelles were analyzed through the density distributions of components and the molecular orientations of CTA+ and toluic acid inside the micelles. It was found that the bonding interactions between CTA+ and toluic in spherical and cylindrical micelles are very different. Almost all the ionized toluic acid (PTA−) in the solution at pH 7 was solubilized into the micelles, and it was located in the CTA+ headgroups region. Additionally, the bonding between surfactant CTA+ and PTA− was very tight due to the electrostatic interactions. The PTA− that penetrated into the micelles effectively screened the electrostatic repulsion among the cationic headgroups, which is considered to be crucial for maintaining the cylindrical micellar shape. As the pH decreased, the carboxyl groups were protonated. The hydration ability of neutral carboxyl groups weakened, resulting in deeper penetration into the micelles. Meanwhile, their bonding interactions with surfactant headgroups also weakened. Accompanied by the strengthen of electrostatic repulsion among the positive headgroups, the cylindrical micelle was broken into spherical micelles. Our work provided an atomic-level insights into the mechanism of pH-induced structural transitions of a CTAB/p-toluic solution, which is expected to be useful for further understanding the aggregate behavior of mixed cationic surfactants and aromatic acids.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Pamina Kazman ◽  
Ramona M. Absmeier ◽  
Harald Engelhardt ◽  
Johannes Buchner

AbstractIn antibody light chain (AL) amyloidosis, overproduced light chain (LC) fragments accumulate as fibrils in organs and tissues of patients. In vitro, AL fibril formation is a slow process, characterized by a pronounced lag phase. The events occurring during this lag phase are largely unknown. We have dissected the lag phase of a patient-derived LC truncation and identified structural transitions that precede fibril formation. The process starts with partial unfolding of the VL domain and the formation of small amounts of dimers. This is a prerequisite for the formation of an ensemble of oligomers, which are the precursors of fibrils. During oligomerization, the hydrophobic core of the LC domain rearranges which leads to changes in solvent accessibility and rigidity. Structural transitions from an anti-parallel to a parallel β-sheet secondary structure occur in the oligomers prior to amyloid formation. Together, our results reveal a rate-limiting multi-step mechanism of structural transitions prior to fibril formation in AL amyloidosis, which offers, in the long run, opportunities for therapeutic intervention.


Small ◽  
2021 ◽  
pp. 2104571
Author(s):  
Abdallah Nassereddine ◽  
Qing Wang ◽  
David Loffreda ◽  
Christian Ricolleau ◽  
Damien Alloyeau ◽  
...  

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