Closing loop base pairs in RNA loop–loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations

2004 ◽  
Vol 10 (5-6) ◽  
pp. 408-417 ◽  
Author(s):  
Jérôme Golebiowski ◽  
Serge Antonczak ◽  
Juan Fernandez-Carmona ◽  
Roger Condom ◽  
Daniel Cabrol-Bass
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Interaction Energy ◽  
Structural Behavior ◽  
Base Pairs ◽  
Dynamics Simulations ◽  
Solvation Analysis

Scaling relations for the interactions between curved graphene sheets in water

2017 ◽  
Vol 19 (44) ◽  
pp. 30217-30226 ◽  
Author(s):  
Sonal Kumar ◽  
Prasad Rama ◽  
Ajay Singh Panwar
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Interaction Energy ◽  
Scaling Relations ◽  
Graphene Sheets ◽  
Dynamics Simulations

The scaling of interaction energy between curved graphene sheets in water with sheet radius and separation was calculated by molecular dynamics simulations.

Binding patterns and dynamics of double-stranded DNA on the phosphorene surface

Nanoscale ◽  
2020 ◽  
Vol 12 (17) ◽  
pp. 9430-9439 ◽  
Author(s):  
Baoyu Li ◽  
Xuejie Xie ◽  
Guangxin Duan ◽  
Serena H. Chen ◽  
Xuan-Yu Meng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Base Pairs ◽  
Upright Orientation ◽  
Double Stranded Dna ◽  
Dynamics Simulations

Molecular dynamics simulations and electrophoresis experiments show that dsDNA can form a stable binding on the phosphorene surface through the terminal base pairs and adopt an upright orientation regardless of its initial configurations.

scholarly journals Molecular dynamics simulations of CH4 diffusion in kaolinite: influence of water content

2019 ◽  
Vol 6 (4) ◽  
pp. 556-563 ◽  
Author(s):  
Bin Zhang ◽  
Jianting Kang ◽  
Tianhe Kang ◽  
Guanxian Kang ◽  
Guofei Zhao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Water Content ◽  
Interaction Energy ◽  
Water Molecules ◽  
Fast Diffusion ◽  
Influence Of Water ◽  
Dynamics Simulations ◽  
Lower Water Content ◽  
Water Contents

Abstract Understanding the interaction of CH4 with kaolinite is significant for researchers in the fields of coalbed CH4 and shale gas. The diffusion behaviors of CH4 in kaolinite with water contents ranging from 0 to 5 wt% have been analyzed by molecular dynamics simulations. The results of the simulations indicate that CH4 molecules can jump between adjacent holes in the kaolinite matrix. CH4 diffusion coefficient was very low (3.28 × 10−9 m2/s) and increased linearly with the increasing of water content. As the water content decreased, the value of radial distribution function first peak between CH4 and oxygen was larger, meaning that with lower water content, the interaction energy between CH4 and oxygen in kaolinite is stronger. The interaction between CH4 and water is linearly positively correlated with water content, in contrast, the interaction energy between kaolinite and water as well as between kaolinite and CH4 decreased linearly with increasing water content. On the other hand, the diffusion of CH4 molecules adsorbed on the surfaces also can be accelerated by the fast diffusion of water molecules in the middle micropore of the kaolinite.

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