Determination of the charge profile in the KcsA selectivity filter using ab initio calculations and molecular dynamics simulations

2009 ◽  
Vol 11 (38) ◽  
pp. 8606 ◽  
Author(s):  
Sebastian Kraszewski ◽  
Céline Boiteux ◽  
Christophe Ramseyer ◽  
Claude Girardet
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Selectivity Filter ◽  
Dynamics Simulations

scholarly journals Surface energy of nanoparticles – influence of particle size and structure

2018 ◽  
Vol 9 ◽  
pp. 2265-2276 ◽  
Author(s):  
Dieter Vollath ◽  
Franz Dieter Fischer ◽  
David Holec
Keyword(s):  
Molecular Dynamics ◽  
Particle Size ◽  
Surface Energy ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Definition Of ◽  
Dynamics Simulations ◽  
Classical Thermodynamics ◽  
A Minor

The surface energy, particularly for nanoparticles, is one of the most important quantities in understanding the thermodynamics of particles. Therefore, it is astonishing that there is still great uncertainty about its value. The uncertainty increases if one questions its dependence on particle size. Different approaches, such as classical thermodynamics calculations, molecular dynamics simulations, and ab initio calculations, exist to predict this quantity. Generally, considerations based on classical thermodynamics lead to the prediction of decreasing values of the surface energy with decreasing particle size. This phenomenon is caused by the reduced number of next neighbors of surface atoms with decreasing particle size, a phenomenon that is partly compensated by the reduction of the binding energy between the atoms with decreasing particle size. Furthermore, this compensating effect may be expected by the formation of a disordered or quasi-liquid layer at the surface. The atomistic approach, based either on molecular dynamics simulations or ab initio calculations, generally leads to values with an opposite tendency. However, it is shown that this result is based on an insufficient definition of the particle size. A more realistic definition of the particle size is possible only by a detailed analysis of the electronic structure obtained from initio calculations. Except for minor variations caused by changes in the structure, only a minor dependence of the surface energy on the particle size is found. The main conclusion of this work is that surface energy values for the equivalent bulk materials should be used if detailed data for nanoparticles are not available.

Insights into water-mediated ion clustering in aqueous CaSO4 solutions: pre-nucleation cluster characteristics studied by ab initio calculations and molecular dynamics simulations

2017 ◽  
Vol 19 (18) ◽  
pp. 11390-11403 ◽  
Author(s):  
Hui-Ji Li ◽  
Dan Yan ◽  
Hou-Qin Cai ◽  
Hai-Bo Yi ◽  
Xiao-Bo Min ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Water Molecules ◽  
Typical Species ◽  
Dynamics Simulations

Neutral clusters are typical species in pre-nucleation processes; the dynamics of water molecules around CaSO4 clusters slow down due to dual reorientation.

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