Molecular Dynamics Simulations of a Charged Dendrimer in Multivalent Salt Solution

2009 ◽  
Vol 113 (40) ◽  
pp. 13161-13170 ◽  
Author(s):  
Wen-de Tian ◽  
Yu-qiang Ma
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Salt Solution ◽  
Dynamics Simulations

Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution

2021 ◽  
Author(s):  
Jingjing Xue ◽  
Xinpeng Li ◽  
Rongri Tan ◽  
Wenjun Zong
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Salt Solution ◽  
Dna Structure ◽  
High Concentration ◽  
Bivalent Metal ◽  
Bivalent Metal Ions ◽  
The Stability ◽  
Dynamics Simulations

Abstract A-DNA is one of the biologically active double helical structure. The study of A-DNA structure has an extensive application for developing the field of DNA packaging in biotechnology. In aqueous solution, the A-DNA structure will have a free transformation, the A-DNA structure will be translated into B-form structure with the evolution of time, and eventually stabilized in the the B-DNA structure. To explore the stability function of the bivalent metal ions on the A-DNA structure, a series of molecular dynamics simulations have been performed on the A-DNA of sequence (CCCGGCCGGG). The results show that bivalent metal ions (Mg2+, Zn2+, Ca2+) generate a great effect on the structural stability of A-DNA in the environment of high concentration. As the interaction between metal ions and electronegative DNA chains, the stability of A-DNA in solution is gradually improved with the increasing of the solution concentration of ions. In metal salt solution with high concentration, metal ions can be easily distributed in the solvation shells around the phosphate groups and further lead to the formation of shorter and more compact DNA structure. Also, in the condition of the same concentration and valency of the metal ions, the stability of A-DNA structure is different. The calculations indicate that the structure of A-DNA in CaCl2 solution is less stable than in MgCl2 and ZnCl2 solution.

Capture of Charged Polymer in Salt Solution

2013 ◽  
Vol 562-565 ◽  
pp. 1296-1301
Author(s):  
Xiao Long Wei ◽  
Jing Jie Sha ◽  
Yun Fei Chen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Salt Solution ◽  
Capture Rate ◽  
Dna Molecules ◽  
High Concentration ◽  
Electrical Field ◽  
Charged Polymer ◽  
Dynamics Simulations ◽  
Increasing Temperature

To understand the capture of charged polymer in salt solution, we investigated the effect of the temperature, concentration of DNA molecules and electrical field to the polynucleotide capture rate by using a single graphene nanopore. From the result of the molecular dynamics simulations, it suggested that the capture rate becomes higher with increasing temperature and that it increases exponentially with the electrical field, and that low and high concentration of the polymer do not exhibit optimal capture rate. By analyzing the simulations results we predict that the capture rate is related to the aperture and the structure of the pore.

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