An evaluation of non-periodic boundary condition models in molecular dynamics simulations using prion octapeptides as probes

2006 ◽  
Vol 760 (1-3) ◽  
pp. 91-98 ◽  
Author(s):  
Eva-Stina Riihimäki ◽  
José Manuel Martínez ◽  
Lars Kloo
Keyword(s):  
Molecular Dynamics ◽  
Boundary Condition ◽  
Molecular Dynamics Simulations ◽  
Periodic Boundary Condition ◽  
Periodic Boundary ◽  
Dynamics Simulations

Heat Transfer on Walls in Molecular Dynamics Simulations: Modelling With Vibrating Reflective Walls

2008 ◽  
Author(s):  
E. A. T. van den Akker ◽  
A. J. H. Frijns ◽  
A. A. van Steenhoven ◽  
P. A. J. Hilbers
Keyword(s):  
Heat Transfer ◽  
Molecular Dynamics ◽  
Boundary Condition ◽  
Heat Exchange ◽  
Molecular Dynamics Simulations ◽  
A Priori ◽  
Computation Time ◽  
Good Choice ◽  
Competitive Model ◽  
Dynamics Simulations

In simulations of micro channel cooling, the heat exchange from fluid to channel wall is an important aspect. Hence the heat exchange should be included in the model. Although numerically very expensive, it can be done by using a molecular wall. Numerically cheap implementations of a wall are the reflective wall and the thermal wall, and the combination of both, the diffusive-specular wall. In this paper we introduce the concept of a vibrating reflective wall as a boundary condition for molecular dynamics simulations. It is shown that the heat transfer with the vibrating reflective wall is the same as with a molecular wall, and that computation time is reduced greatly. As a competitive model, the diffusive-specular boundary condition is analyzed; it is shown that a good choice of parameters can give similar results in the same computation time, but the choice of parameters is not known a priori, therefore the vibrating reflective wall boundary condition is preferable.

Toward Rational Design of Fast Ion Conductors: Molecular Dynamics Modeling of Interfaces of Nanoscale Planar Heterostructures

2002 ◽  
Vol 17 (7) ◽  
pp. 1686-1691 ◽  
Author(s):  
J-J. Liang ◽  
P.W-C. Kung
Keyword(s):  
Molecular Dynamics ◽  
Ionic Conductivity ◽  
Periodic Boundary Condition ◽  
Rational Design ◽  
Periodic Boundary ◽  
Dynamics Modeling ◽  
Molecular Dynamics Modeling ◽  
Conductivity Increase ◽  
Dynamics Simulations ◽  
Fast Ion

Increased ionic conductivity at nanoscale planar interfaces of the CaF2|BaF2 system was successfully modeled using molecular dynamics simulations. A criterion was established to construct simulation cells containing any arbitrarily lattice-mismatched interfaces while permitting periodic boundary condition. The relative (to the bulk) ionic conductivity increase at the 111 (CaF2)|111 (BaF2) interface was qualitatively reproduced. Higher conductivity, by a factor of 7.6, was predicted for the 001 (CaF2)|001 (BaF2) interface. A crystalline nanocomposite of the CaF2|BaF2 system, in which the [001] morphology is encouraged and crystallite dimensions are approximately 4 nm, was proposed to give ionic conductivity approaching that predicted for the 001 (CaF2)|001 (BaF2) interface.

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