Steady-State Statistical Sputtering Model for Extracting Depth Profiles from Molecular Dynamics Simulations of Dynamic SIMS

2011 ◽  
Vol 116 (1) ◽  
pp. 1042-1051 ◽  
Author(s):  
Robert J. Paruch ◽  
Zbigniew Postawa ◽  
Andreas Wucher ◽  
Barbara J. Garrison
Keyword(s):  
Molecular Dynamics ◽  
Steady State ◽  
Molecular Dynamics Simulations ◽  
Depth Profiles ◽  
Dynamics Simulations

Site Balance Models in Plasma Processing: A Comparison to Molecular Dynamics Simulations

1995 ◽  
Vol 389 ◽  
Author(s):  
M.E. Barone ◽  
D.B. Graves
Keyword(s):  
Molecular Dynamics ◽  
Steady State ◽  
Molecular Dynamics Simulations ◽  
Phenomenological Models ◽  
Silicon Surface ◽  
Plasma Processing ◽  
Md Simulations ◽  
Balance Model ◽  
Dynamics Simulations ◽  
A Site

ABSTRACTMolecular dynamics (MD) simulations were conducted of Cl+ impact (at 10, 25 and 50 eV) of an initially bare silicon surface, leading to steady state coverage of Cl in a mixed chlorosilyl layer. Our main goal in this study was to compare the MD predictions to models of ion-assisted etching involving the concept of a site balance. For the case of 50 eV Cl+ etching silicon, the coverage vs. exposure results in the simulation could be reasonably well reproduced in a site balance model, but only if the correct parameters in the model were taken from the simulation. The results of the comparison suggest that MD simulations can be helpful in the development of physically sound phenomenological models of ion-assisted etching.

scholarly journals On the Lifetimes of Antisteady States

1996 ◽  
Vol 49 (1) ◽  
pp. 39 ◽  
Author(s):  
Debra J Searles ◽  
Denis J Evans
Keyword(s):  
Molecular Dynamics ◽  
Steady State ◽  
Lyapunov Exponent ◽  
Molecular Dynamics Simulations ◽  
State System ◽  
Nonequilibrium Molecular Dynamics ◽  
Trajectory Error ◽  
Dynamics Simulations ◽  
Lyapunov Instability

The influence of Lyapunov instability on the lifetimes of antisteady states is investigated using nonequilibrium molecular dynamics simulations. It is found that the lifetime is inversely proportional to the smallest Lyapunov exponent of the steady state system and proportional to the logarithm of the trajectory error per timestep.

Variation in aspects of cysteine proteinase catalytic mechanism deduced by spectroscopic observation of dithioester intermediates, kinetic analysis and molecular dynamics simulations

2001 ◽  
Vol 357 (2) ◽  
pp. 343-352 ◽  
Author(s):  
James D. REID ◽  
Syeed HUSSAIN ◽  
Suneal K. SREEDHARAN ◽  
Tamara S. F. BAILEY ◽  
Surapong PINITGLANG ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Steady State ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Catalytic Mechanism ◽  
Cysteine Proteinase ◽  
Salt Bridge ◽  
Dynamics Simulation ◽  
Active Centre ◽  
Dynamics Simulations

The possibility of a slow post-acylation conformational change during catalysis by cysteine proteinases was investigated by using a new chromogenic substrate, N-acetyl-Phe-Gly methyl thionoester, four natural variants (papain, caricain, actinidin and ficin), and stopped-flow spectral analysis to monitor the pre-steady state formation of the dithioacylenzyme intermediates and their steady state hydrolysis. The predicted reversibility of acylation was demonstrated kinetically for actinidin and ficin, but not for papain or caricain. This difference between actinidin and papain was investigated by modelling using QUANTA and CHARMM. The weaker binding of hydrophobic substrates, including the new thionoester, by actinidin than by papain may not be due to the well-known difference in their S2-subsites, whereby that of actinidin in the free enzyme is shorter due to the presence of Met211. Molecular dynamics simulation suggests that during substrate binding the sidechain of Met211 moves to allow full access of a Phe sidechain to the S2-subsite. The highly anionic surface of actinidin may contribute to the specificity difference between papain and actinidin. During subsequent molecular dynamics simulations the P1 product, methanol, diffuses rapidly (over < 8ps) out of papain and caricain but ‘lingers’ around the active centre of actinidin. Uniquely in actinidin, an Asp142–Lys145 salt bridge allows formation of a cavity which appears to constrain diffusion of the methanol away from the catalytic site. The cavity then undergoes large scale movements (over 4.8 Å) in a highly correlated manner, thus controlling the motions of the methanol molecule. The changes in this cavity that release the methanol might be those deduced kinetically.

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