Stoichiometry tuning of TaN films through ion treatment: Molecular dynamics study

2021 ◽  
Vol 39 (6) ◽  
pp. 062601
Author(s):  
Jaipal Methary ◽  
Rajesh Sathiyanarayanan ◽  
Rui Li ◽  
Phillip J. Stout
Keyword(s):  
Molecular Dynamics ◽  
Ion Treatment

scholarly journals EFFECT OF THE ION TREATMENT ON AN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY

2012 ◽  
Vol 12 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Elisabeth Catherina Widjajakusuma ◽  
Alessandra Villa ◽  
Gerhard Stock
Keyword(s):  
Molecular Dynamics ◽  
Structural Difference ◽  
Md Simulations ◽  
Field Method ◽  
Ion Concentration ◽  
Reaction Field ◽  
The Stability ◽  
Ion Treatment ◽  
Rna Hairpin ◽  
Amber Force Fields

Molecular dynamics has been employed to study the effect of ion treatment on the stability of 14-nucleotide RNA hairpin of Coxsackievirus B3. Three AMBER force fields were used: AMBER94, AMBER98, and AMBER99, which showed no significant structural difference of the hairpin. Thereafter, we applied two different long-range electrostatic treatments that were reaction field and PME methods, and calculated the distribution of ions around the hairpin. Although the structural stabilities of the MD simulations using both methods were similar in 0.14 M Na+, ion environment around the hairpin was notably different. In particular, structural stabilition of the hairpin with increasing ion concentration and with ion Mg2+ cannot be accommodated by simulations using reaction field method. Furthermore, the MD simulations using PME method suggested the strong similarity in structural and dynamical properties of the hairpin with 0.14 M Na+, 0.50 M Na+, 1,03 M Na+, and 0.08 M Mg2+ concentrations. However, the simulations revealed different ion occupations of Na+ and Mg2+.

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