Computer simulations of protein folding by targeted molecular dynamics

2000 ◽  
Vol 39 (3) ◽  
pp. 252-260 ◽  
Author(s):  
Philippe Ferrara ◽  
Joannis Apostolakis ◽  
Amedeo Caflisch
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Computer Simulations ◽  
Targeted Molecular Dynamics

scholarly journals Simulation of Mechanical Deformation and Tribology of Nano-Thin Amorphous Hydrogenated Carbon (a:Ch) Films Using Molecular Dynamics

1996 ◽  
Vol 436 ◽  
Author(s):  
J. N. Glosli ◽  
M. R. Philpott ◽  
J. Belak
Keyword(s):  
Molecular Dynamics ◽  
Substrate Temperature ◽  
Computer Simulations ◽  
Mechanical Deformation ◽  
Porous Graphite ◽  
Pure Carbon ◽  
Substrate Temperatures ◽  
Amorphous Hydrogenated Carbon ◽  
Deposition Energy

AbstractMolecular dynamics computer simulations are used to study the effect of substrate temperature on the microstructure of deposited amorphous hydrogenated carbon (a:CH) films. A transition from dense diamond-like films to porous graphite-like films is observed between substrate temperatures of 400K and 600K for a deposition energy of 20 eV. The dense a:CH film grown at 300K and 20 eV has a hardness (˜50 GPa) about half that of a pure carbon (a:C) film grown under the same conditions.

Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent

2016 ◽  
Vol 18 (18) ◽  
pp. 13052-13065 ◽  
Author(s):  
Emanuel K. Peter ◽  
Joan-Emma Shea ◽  
Igor V. Pivkin
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Protein Folding ◽  
Kinetic Monte Carlo ◽  
Replica Exchange ◽  
Replica Exchange Molecular Dynamics ◽  
Accelerated Simulation ◽  
Explicit Solvent ◽  
Exchange Algorithms

In this paper, we present a coarse replica exchange molecular dynamics (REMD) approach, based on kinetic Monte Carlo (kMC).

Computer Simulation Studies of Fracture in Vitreous Silica

2002 ◽  
Vol 731 ◽  
Author(s):  
Romulo Ochoa ◽  
Michael Arief ◽  
Joseph H. Simmons
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Computer Simulations ◽  
Silica Glass ◽  
Vitreous Silica ◽  
Uniaxial Strain ◽  
Force Function ◽  
Simulation Studies ◽  
Previous Fracture ◽  
Computer Simulation Studies

AbstractWe conduct molecular dynamics computer simulations of fracture in silica glass using the van Beest, Kramer, and van Santen model. Stress is applied by uniaxial strain at different pulling rates. Comparisons with previous fracture simulations of silica that used the Soules force function are presented. We find that in both models stress is relieved by rotation of the (SiO4)-2 tetrahedrons, increasing Si-O-Si bonding angles, and only small changes in the tetrahedron dimensions and O-Si-O angles.

Sign in / Sign up

Export Citation Format

Share Document