scholarly journals Real-time tracking of ionic nano-domains under shear flow

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Clodomiro Cafolla ◽  
Kislon Voïtchovsky

AbstractThe behaviour of ions at solid–liquid interfaces underpins countless phenomena, from the conduction of nervous impulses to charge transfer in solar cells. In most cases, ions do not operate as isolated entities, but in conjunction with neighbouring ions and the surrounding solution. In aqueous solutions, recent studies suggest the existence of group dynamics through water-mediated clusters but results allowing direct tracking of ionic domains with atomic precision are scarce. Here, we use high-speed atomic force microscopy to track the evolution of Rb+, K+, Na+ and Ca2+ nano-domains containing 20 to 120 ions adsorbed at the surface of mica in aqueous solution. The interface is exposed to a shear flow able to influence the lateral motion of single ions and clusters. The results show that, when in groups, metal ions tend to move with a relatively slow dynamics, as can be expected from a correlated group motion, with an average residence timescale of ~ 1–2 s for individual ions at a given atomic site. The average group velocity of the clusters depends on the ions’ charge density and can be explained by the ion’s hydration state. The lateral shear flow of the fluid is insufficient to desorb ions, but indirectly influences the diffusion dynamics by acting on ions in close vicinity to the surface. The results provide insights into the dynamics of ion clusters when adsorbed onto an immersed solid under shear flow.

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Rina Hirano ◽  
Yasuhiro Arimura ◽  
Tomoya Kujirai ◽  
Mikihiro Shibata ◽  
Aya Okuda ◽  
...  

AbstractH2A.B is an evolutionarily distant histone H2A variant that accumulates on DNA repair sites, DNA replication sites, and actively transcribing regions in genomes. In cells, H2A.B exchanges rapidly in chromatin, but the mechanism has remained enigmatic. In the present study, we found that the H2A.B-H2B dimer incorporated within the nucleosome exchanges with the canonical H2A-H2B dimer without assistance from additional factors, such as histone chaperones and nucleosome remodelers. High-speed atomic force microscopy revealed that the H2A.B nucleosome, but not the canonical H2A nucleosome, transiently forms an intermediate “open conformation”, in which two H2A.B-H2B dimers may be detached from the H3-H4 tetramer and bind to the DNA regions near the entry/exit sites. Mutational analyses revealed that the H2A.B C-terminal region is responsible for the adoption of the open conformation and the H2A.B-H2B exchange in the nucleosome. These findings provide mechanistic insights into the histone exchange of the H2A.B nucleosome.


2006 ◽  
Vol 45 (3B) ◽  
pp. 1897-1903 ◽  
Author(s):  
Toshio Ando ◽  
Takayuki Uchihashi ◽  
Noriyuki Kodera ◽  
Atsushi Miyagi ◽  
Ryo Nakakita ◽  
...  

2011 ◽  
Vol 47 (17) ◽  
pp. 4974 ◽  
Author(s):  
Shigeto Inoue ◽  
Takayuki Uchihashi ◽  
Daisuke Yamamoto ◽  
Toshio Ando

Nano Research ◽  
2015 ◽  
Vol 8 (7) ◽  
pp. 2170-2178 ◽  
Author(s):  
Zaixing Jiang ◽  
Shuai Zhang ◽  
Chuanxu Yang ◽  
Jørgen Kjems ◽  
Yudong Huang ◽  
...  

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