Analysis of Water Molecules in the Hras-GTP and GDP Complexes with Molecular Dynamics Simulations

2013 ◽  
pp. 351-360
Author(s):  
Takeshi Miyakawa ◽  
Ryota Morikawa ◽  
Masako Takasu ◽  
Akira Dobashi ◽  
Kimikazu Sugimori ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Water Molecules ◽  
Dynamics Simulations

scholarly journals Origin and control of ionic hydration patterns in nanopores

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Miraslau L. Barabash ◽  
William A. T. Gibby ◽  
Carlo Guardiani ◽  
Alex Smolyanitsky ◽  
Dmitry G. Luchinsky ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Water Molecules ◽  
Surrounding Water ◽  
Ionic Hydration ◽  
Hydration Shells ◽  
Water Layers ◽  
Dynamics Simulations ◽  
And Control

AbstractIn order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. Here, we study the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in a graphene nanopore in terms of experimentally accessible radial distribution functions, giving results that agree well with molecular dynamics simulations. The patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the graphene membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns.

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.

Anomalous diffusion of water molecules at grain boundaries in ice Ih

2018 ◽  
Vol 20 (20) ◽  
pp. 13944-13951 ◽  
Author(s):  
Pedro Augusto Franco Pinheiro Moreira ◽  
Roberto Gomes de Aguiar Veiga ◽  
Ingrid de Almeida Ribeiro ◽  
Rodrigo Freitas ◽  
Julian Helfferich ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Grain Boundaries ◽  
Anomalous Diffusion ◽  
First Principles ◽  
Water Molecules ◽  
Diffusive Behavior ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

First-principles and classical molecular dynamics simulations show that diffusion of water molecules at pre-melted grain boundaries in ice is glassy-like, showing sub-diffusive behavior.

Molecular Dynamics Simulations of the Conductivity of Aqueous NaCl in the Presence of Sucrose and Electric Fields

2014 ◽  
Vol 937 ◽  
pp. 200-206
Author(s):  
Xiao Gang Li ◽  
Shu Ai Yang ◽  
Ming Jun Tang ◽  
Jing Lei ◽  
Hui Hu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Electric Fields ◽  
Ion Pairs ◽  
Water Molecules ◽  
Flashover Voltage ◽  
Low Humidity ◽  
Natural Contamination ◽  
Dynamics Simulations ◽  
Contact Ion Pairs

Various natural contamination components distributed on the surface of high-voltage insulators play important roles on the flashover hazard. Under the low humidity condition, the flashover voltage could be affected considerably by the sucrose contaminations. Molecular dynamics simulations have been carried out in order to reveal the microscopic mechanisms for the sucrose-involved flashover uptake. It is found that the diffusion of ions decreases significantly and thus the conductivity of aqueous medium is lowered apparently. In the presence of sucrose, the contact ion pairs formed between Na+ and Cl- ions are enhanced because both ions are less coordinated to water molecules. The influence of the external electric fields on the diffusion and conductivity were investigated as well. It is suggested that the sucrose contamination might lead to the uneven electric fields on the insulator surface.

Insights into structural and dynamical features of water at halloysite interfaces probed by DFT and classical molecular dynamics simulations

2016 ◽  
Vol 18 (3) ◽  
pp. 2164-2174 ◽  
Author(s):  
Davide Presti ◽  
Alfonso Pedone ◽  
Giordano Mancini ◽  
Celia Duce ◽  
Maria Rosaria Tiné ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Water Molecules ◽  
Functional Theory ◽  
Structure And Dynamics ◽  
Classical Molecular Dynamics ◽  
Dynamical Features ◽  
Dynamics Simulations

Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension.

scholarly journals Molecular Dynamics Simulations of the Interaction between Water Molecules and Aggregates of Acetic or Propionic Acid Molecules

2015 ◽  
Vol 119 (51) ◽  
pp. 15662-15674 ◽  
Author(s):  
Bastien Radola ◽  
Sylvain Picaud ◽  
Delphine Vardanega ◽  
Pál Jedlovszky
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Propionic Acid ◽  
Water Molecules ◽  
Dynamics Simulations
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