scholarly journals Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics

2015 ◽  
Vol 43 (4) ◽  
pp. 2412-2423 ◽  
Author(s):  
Marco Pasi ◽  
John H. Maddocks ◽  
Richard Lavery
Keyword(s):  
Molecular Dynamics ◽  
Dna Sequence ◽  
Potassium Ion ◽  
Sequence Dependence ◽  
Ion Distributions

DFT study of DNA sequence dependence at the level of dinucleoside monophosphates

2011 ◽  
Vol 975 (1-3) ◽  
pp. 69-75 ◽  
Author(s):  
V.I. Poltev ◽  
V.M. Anisimov ◽  
V.I. Danilov ◽  
D. Garcia ◽  
A. Deriabina ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dft Study ◽  
Sequence Dependence ◽  
Dinucleoside Monophosphates

Molecular Dynamics Study of Confined Fluid in Graphene Nanopores

2014 ◽  
Vol 1061-1062 ◽  
pp. 205-208
Author(s):  
Kun Li ◽  
Jing Jie Sha ◽  
Lei Liu ◽  
Gen Sheng Wu ◽  
Wei Si ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Field Strength ◽  
Electric Field ◽  
Electric Field Strength ◽  
Ionic Currents ◽  
Md Simulations ◽  
Solution Concentration ◽  
Main Peak ◽  
Ion Distributions ◽  
Solvent Molecules

With the miniaturization of the NEMS/MEMS, the size effect becomes significant in the nanochannels/nanopores through which fluid flows as well as the interface effect. By all-atom molecular dynamics (MD) simulations, the ion transportation is investigated in nanopores as well as the physical properties at solid-liquid interface. To describe the anion and cation distributions of NaCl solution in vicinity of graphene nanopores, a new MD model was developed, taking thermal vibration of wall atoms, the structure of solvent molecules and ion sizes into consideration. The main peak locations of ion distributions stayed unchanged by changing the nanopore size, the solution concentration and the electric field strength. The ionic currents increased linearly with the diameter and the electric field strength, while it increased non-linearly with the solution concentration.

scholarly journals The DNA Sequence-dependence of Nucleosome Positioningin vivoandin vitro

2010 ◽  
Vol 27 (6) ◽  
pp. 713-724 ◽  
Author(s):  
Andrew Travers ◽  
Edwige Hiriart ◽  
Mark Churcher ◽  
Micaela Caserta ◽  
Ernesto Di Mauro
Keyword(s):  
Dna Sequence ◽  
Sequence Dependence
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