scholarly journals Molecular dynamics simulations of RNA: Anin silico single molecule approach

Biopolymers ◽  
2007 ◽  
Vol 85 (2) ◽  
pp. 169-184 ◽  
Author(s):  
S. Elizabeth McDowell ◽  
Nad'a Špačková ◽  
Jiří Šponer ◽  
Nils G. Walter
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Single Molecule ◽  
Dynamics Simulations

Single glucose molecule transport process revealed by force tracing and molecular dynamics simulations

2018 ◽  
Vol 3 (5) ◽  
pp. 517-524 ◽  
Author(s):  
Yangang Pan ◽  
Yuebin Zhang ◽  
Pianchou Gongpan ◽  
Qingrong Zhang ◽  
Siteng Huang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Glucose Transport ◽  
Single Molecule ◽  
Transport Process ◽  
Theoretical Methods ◽  
Molecule Transport ◽  
Glucose Molecule ◽  
Dynamics Simulations

Single-molecule glucose transport was illuminated using both experimental and theoretical methods.

Molecular Dynamics Simulations of Water and Ion Structures Near Charged Surfaces

2007 ◽  
Author(s):  
Dongyan Xu ◽  
Deyu Li ◽  
Yongsheng Leng
Keyword(s):  
Molecular Dynamics ◽  
Surface Charge ◽  
Molecular Dynamics Simulations ◽  
Single Molecule ◽  
Research Field ◽  
Water Molecules ◽  
Wall Region ◽  
Surface Charges ◽  
Ion Distribution ◽  
Dynamics Simulations

Extensive research has been devoted to nanofluidics in the past decade because of its potential applications in single molecule sensing and manipulations. Fundamental studies have attracted significant attention in this research field since the success of nanofluidic devices depends on a thorough understanding of the fluidic, ionic, and molecular behavior in highly confined nano-environments. In this paper, we report on molecular dynamics simulations of the effect of surface charge densities on the ion distribution and the water density profile close to a charged surface. We demonstrate that surface charges not only interact with mobile ions in the electrolyte, but also interact with water molecules due to their polarizability, and hence influence the orientation of water molecules in the near wall region. For the first time, we show that as the surface charge density increases, the water molecules within ∼ 5 Å of the {100} silicon surface will evolve from one layer into two layers. Meanwhile, the orientation of the water molecules is more aligned instead of randomly distributed. This layering effect may have important implications on electroosmotic flow through nanochannels and heat transfer across the solid-liquid interface.

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