Molecular Dynamics Studies of the Conformational Preferences of a DNA Double Helix in Water and an Ethanol/Water Mixture:  Theoretical Considerations of the A ⇔ B Transition

1998 ◽  
Vol 102 (23) ◽  
pp. 4658-4667 ◽  
Author(s):  
D. Sprous ◽  
M. A. Young ◽  
D. L. Beveridge
Keyword(s):  
Molecular Dynamics ◽  
Double Helix ◽  
Water Mixture ◽  
Conformational Preferences ◽  
Dna Double Helix ◽  
Theoretical Considerations

A Nanosecond Molecular Dynamics Trajectory for a B DNA Double Helix: Evidence for Substates

1994 ◽  
Vol 116 (10) ◽  
pp. 4461-4462 ◽  
Author(s):  
K. J. McConnell ◽  
R Nirmala ◽  
M. A. Young ◽  
G. Ravishanker ◽  
D. L. Beveridge
Keyword(s):  
Molecular Dynamics ◽  
Double Helix ◽  
Molecular Dynamics Trajectory ◽  
Dna Double Helix

scholarly journals Positively and Negatively Hydrated Counterions in Molecular Dynamics Simulations of DNA Double Helix

2020 ◽  
Vol 65 (6) ◽  
pp. 510
Author(s):  
S. Perepelytsya
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Double Helix ◽  
Dipole Moments ◽  
Hydration Shell ◽  
Minor Groove ◽  
Water Molecules ◽  
Negative Hydration ◽  
Dynamics Simulations ◽  
Dna Double Helix

The DNA double helix is a polyanionic macromolecule that is neutralized in water solutions by metal ions (counterions). The property of counterions to stabilize the water network (positive hydration) or to make it friable (negative hydration) is important in terms of the physical mechanisms of stabilization of the DNA double helix. In the present research, the effects of positive hydration of Na+ counterions and negative hydration of K+ and Cs+ counterions incorporated into the hydration shell of the DNA double helix have been studied using molecular dynamics simulations. The results have shown that the dynamics of the hydration shell of counterions depends on the region of the double helix: minor groove, major groove, and outside the macromolecule. The longest average residence time has been observed for water molecules contacting with the counterions localized in the minor groove of the double helix (about 50 ps for Na+ and lower than 10 ps for K+ and Cs+). The estimated potentials of the mean force for the hydration shells of counterions show that the water molecules are constrained too strongly, and the effect of negative hydration for K+ and Cs+ counterions has not been observed in the simulations. The analysis has shown that the effects of counterion hydration can be described more accurately with water models having lower dipole moments.

scholarly journals Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings

2019 ◽  
Vol 10 (30) ◽  
pp. 7200-7211 ◽  
Author(s):  
Daniele Loco ◽  
Louis Lagardère ◽  
Gérardo A. Cisneros ◽  
Giovanni Scalmani ◽  
Michael Frisch ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Complex Systems ◽  
Large Scale ◽  
Double Helix ◽  
Point Dipole ◽  
Thiazole Orange ◽  
Large Complex ◽  
Dna Double Helix

Hybrid DFT(Gaussian)/AMOEBA(Tinker/Tinker-HP) polarizable molecular dynamics including the QM/MM mutual polarization on large complex systems. Example of the thiazole orange dye buried in a DNA double helix, embedded in a sphere of water (16 500 atoms).

Structurization Of Counterions Around DNA Double Helix: A Molecular Dynamics Study

2015 ◽  
Vol 60 (5) ◽  
pp. 433-442 ◽  
Author(s):  
O.O. Liubysh ◽  
◽  
A.V. Vlasiuk ◽  
S.M. Perepelytsya ◽  
◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Double Helix ◽  
Dna Double Helix
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