The DNA-esperamicin A1 complex. A model based on solvated molecular dynamics simulations

1994 ◽  
Vol 116 (1) ◽  
pp. 15-29 ◽  
Author(s):  
D. R. Langley ◽  
J. Golik ◽  
B. Krishman ◽  
T. W. Doyle ◽  
D. L. Beveridge
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Model Based ◽  
Dynamics Simulations

scholarly journals Pore translocation of knotted DNA rings

2017 ◽  
Vol 114 (15) ◽  
pp. E2991-E2997 ◽  
Author(s):  
Antonio Suma ◽  
Cristian Micheletti
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Model Based ◽  
Translocation Velocity ◽  
Dynamics Simulations

We use an accurate coarse-grained model for DNA and stochastic molecular dynamics simulations to study the pore translocation of 10-kbp–long DNA rings that are knotted. By monitoring various topological and physical observables we find that there is not one, as previously assumed, but rather two qualitatively different modes of knot translocation. For both modes the pore obstruction caused by knot passage has a brief duration and typically occurs at a late translocation stage. Both effects are well in agreement with experiments and can be rationalized with a transparent model based on the concurrent tensioning and sliding of the translocating knotted chains. We also observed that the duration of the pore obstruction event is more controlled by the knot translocation velocity than the knot size. These features should advance the interpretation and design of future experiments aimed at probing the spontaneous knotting of biopolymers.

Stability of reverse micelles in rare-earth separation: a chemical model based on a molecular approach

2017 ◽  
Vol 19 (10) ◽  
pp. 7094-7100 ◽  
Author(s):  
Yushu Chen ◽  
Magali Duvail ◽  
Philippe Guilbaud ◽  
Jean-François Dufrêche
Keyword(s):  
Molecular Dynamics ◽  
Rare Earth ◽  
Molecular Dynamics Simulations ◽  
Reverse Micelles ◽  
Chemical Model ◽  
Molecular Approach ◽  
Organic Solution ◽  
Model Based ◽  
The Stability ◽  
Dynamics Simulations

A new molecular approach based on molecular dynamics simulations is proposed to investigate the stability of reverse micelles containing strategic metals in organic solution.

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