scholarly journals Influence of interaction between Cu adatoms on the hopping diffusion on Cu(001) surface

2006 ◽  
Vol 55 (8) ◽  
pp. 4214
Author(s):  
Wang Yong-Liang ◽  
Zhang Chao ◽  
Tang Xin ◽  
Zhang Qing-Yu
Keyword(s):  
Hopping Diffusion

scholarly journals Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription

2021 ◽  
Vol 22 (5) ◽  
pp. 2398
Author(s):  
Wooyoung Kang ◽  
Seungha Hwang ◽  
Jin Young Kang ◽  
Changwon Kang ◽  
Sungchul Hohng
Keyword(s):  
Single Molecule ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Facilitated Diffusion ◽  
One Dimensional ◽  
Bacterial Transcription ◽  
Fluorescence Measurements ◽  
Dimensional Diffusion ◽  
Single Molecule Studies ◽  
Hopping Diffusion

Two different molecular mechanisms, sliding and hopping, are employed by DNA-binding proteins for their one-dimensional facilitated diffusion on nonspecific DNA regions until reaching their specific target sequences. While it has been controversial whether RNA polymerases (RNAPs) use one-dimensional diffusion in targeting their promoters for transcription initiation, two recent single-molecule studies discovered that post-terminational RNAPs use one-dimensional diffusion for their reinitiation on the same DNA molecules. Escherichia coli RNAP, after synthesizing and releasing product RNA at intrinsic termination, mostly remains bound on DNA and diffuses in both forward and backward directions for recycling, which facilitates reinitiation on nearby promoters. However, it has remained unsolved which mechanism of one-dimensional diffusion is employed by recycling RNAP between termination and reinitiation. Single-molecule fluorescence measurements in this study reveal that post-terminational RNAPs undergo hopping diffusion during recycling on DNA, as their one-dimensional diffusion coefficients increase with rising salt concentrations. We additionally find that reinitiation can occur on promoters positioned in sense and antisense orientations with comparable efficiencies, so reinitiation efficiency depends primarily on distance rather than direction of recycling diffusion. This additional finding confirms that orientation change or flipping of RNAP with respect to DNA efficiently occurs as expected from hopping diffusion.

Two-dimensional hopping diffusion across material interfaces

1994 ◽  
Vol 55 (8) ◽  
pp. 759-766 ◽  
Author(s):  
J. Deppe ◽  
R.F. Wallis ◽  
I. Nachev ◽  
M. Balkanski
Keyword(s):  
Two Dimensional ◽  
Material Interfaces ◽  
Hopping Diffusion

scholarly journals A Fractal-Based Correlation for Time-Dependent Surface Diffusivity in Porous Adsorbents

Processes ◽  
2020 ◽  
Vol 8 (6) ◽  
pp. 689 ◽  
Author(s):  
Vassilis J. Inglezakis ◽  
Marco Balsamo ◽  
Fabio Montagnaro
Keyword(s):  
Surface Diffusion ◽  
Solid Phase ◽  
Time Dependent ◽  
Limited Attention ◽  
Monotonic Trend ◽  
Surface Diffusivity ◽  
Variable Surface ◽  
Adsorption Processes ◽  
Hindered Diffusion ◽  
Hopping Diffusion

Fluid–solid adsorption processes are mostly governed by the adsorbate transport in the solid phase and surface diffusion is often the limiting step of the overall process in microporous materials such as zeolites. This work starts from a concise review of concepts and models for surface transport and variable surface diffusivity. It emerges that the phenomenon of hindered surface diffusion for monolayer adsorption, which is common in zeolites, and models able to fit a non-monotonic trend of surface diffusivity against adsorbate solid phase concentration, have received limited attention. This work contributes to the literature of hindered diffusion by formulating a time-dependent equation for surface diffusivity based on fractal dynamics concepts. The proposed equation takes into account the contributions of both fractal-like diffusion (a time-decreasing term) and hopping diffusion (a time-increasing term). The equation is discussed and numerically analyzed to testify its ability to reproduce the possible different patterns of surface diffusivity vs. time.

scholarly journals Interfacial Properties and Hopping Diffusion of Small Nanoparticle in Polymer/Nanoparticle Composite with Attractive Interaction on Side Group

Polymers ◽  
2018 ◽  
Vol 10 (6) ◽  
pp. 598 ◽  
Author(s):  
Kai-Xin Ren ◽  
Xiang-Meng Jia ◽  
Gui-Sheng Jiao ◽  
Tao Chen ◽  
Hu-Jun Qian ◽  
...  
Keyword(s):  
Interfacial Properties ◽  
Attractive Interaction ◽  
Side Group ◽  
Polymer Nanoparticle ◽  
Hopping Diffusion

scholarly journals Probing inhomogeneous diffusion in the microenvironments of phase-separated polymers under confinement

2018 ◽  
Author(s):  
Marjan Shayegan ◽  
Radin Tahvildari ◽  
Lydia Kisley ◽  
Kimberly Metera ◽  
Stephen W. Michnick ◽  
...  
Keyword(s):  
Rna Binding ◽  
Diffusion Mechanism ◽  
Ribonucleoprotein Complexes ◽  
Non Gaussian ◽  
Separation Of Proteins ◽  
Catalytic Functions ◽  
Hopping Diffusion ◽  
And Control

Biopolymer condensates formed by liquid-liquid phase separation of proteins and nucleic acids have been recently discovered to be prevalent in biology. These dynamic condensates behave like biochemical reaction vessels but little is known about their structural organization and properties. Their biophysical properties and catalytic functions are likely related to condensate size, and thus it is critical that we study them on scales found in vivo. However, previous in vitro studies of condensate assembly and physical properties have involved condensates up to 1000 times larger than those found in vivo. Here, we report the application of confinement microscopy to visualize condensates and control their sizes by creating appropriate confinement length scales relevant to the cell environment. We observe anomalous diffusion of probe particles embedded within confined condensates, as well as heterogeneous dynamics in condensates formed from PEG/dextran and in ribonucleoprotein complexes of RNA and the RNA-binding protein Dhh1. We propose that the non-Gaussian dynamics we observe may indicate a hopping diffusion mechanism inside condensates. We also observe that for dextran-rich condensates, but not for ribonucleo condensates, probe particle diffusion depends on condensate size.

scholarly journals Three-Dimensional Tracking of Interfacial Hopping Diffusion

2017 ◽  
Vol 119 (26) ◽  
Author(s):  
Dapeng Wang ◽  
Haichao Wu ◽  
Daniel K. Schwartz
Keyword(s):  
Three Dimensional ◽  
Hopping Diffusion
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