On the Molecular Mechanism of Drug Intercalation into DNA: A Simulation Study of the Intercalation Pathway, Free Energy, and DNA Structural Changes

2008 ◽  
Vol 130 (30) ◽  
pp. 9747-9755 ◽  
Author(s):  
Arnab Mukherjee ◽  
Richard Lavery ◽  
Biman Bagchi ◽  
James T. Hynes
Keyword(s):  
Free Energy ◽  
Molecular Mechanism ◽  
Simulation Study ◽  
Structural Changes

Molecular mechanism of thiamine pyrophosphate import into mitochondria: a molecular simulation study

2021 ◽  
Author(s):  
F. Van Liefferinge ◽  
E.-M. Krammer ◽  
J. Waeytens ◽  
M. Prévost
Keyword(s):  
Molecular Mechanism ◽  
Molecular Simulation ◽  
Simulation Study ◽  
Thiamine Pyrophosphate

Free energy and scalings for polymer translocation through a nanopore: A molecular dynamics simulation study combined with milestoning

2012 ◽  
Vol 376 (4) ◽  
pp. 290-292 ◽  
Author(s):  
Xiang-Gui Xue ◽  
Li Zhao ◽  
Zhong-Yuan Lu ◽  
Ze-Sheng Li
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Polymer Translocation

Physical origin underlying the prenucleation-cluster-mediated nonclassical nucleation pathways for calcium phosphate

2019 ◽  
Vol 21 (27) ◽  
pp. 14530-14540 ◽  
Author(s):  
Xiao Yang ◽  
Mingzhu Wang ◽  
Yang Yang ◽  
Beiliang Cui ◽  
Zhijun Xu ◽  
...  
Keyword(s):  
Free Energy ◽  
Phase Separation ◽  
Calcium Phosphate ◽  
Molecular Mechanism ◽  
Free Energy Calculations ◽  
Nucleation Process ◽  
Physical Origin ◽  
Energy Calculations

We employed free energy calculations to reveal the molecular mechanism underlying the non-classical nucleation process and phase separation for calcium phosphate.

scholarly journals Molecular mechanism and binding free energy of doxorubicin intercalation in DNA

2019 ◽  
Vol 21 (7) ◽  
pp. 3877-3893 ◽  
Author(s):  
Bahaa Jawad ◽  
Lokendra Poudel ◽  
Rudolf Podgornik ◽  
Nicole F. Steinmetz ◽  
Wai-Yim Ching
Keyword(s):  
Free Energy ◽  
Molecular Mechanism ◽  
Binding Free Energy ◽  
Md Simulations ◽  
Intercalation Process

The intercalation process of binding doxorubicin (DOX) in DNA is studied by extensive MD simulations.

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