Three-dimensional model of the human aromatase enzyme and density functional parameterization of the iron-containing protoporphyrin IX for a molecular dynamics study of heme-cysteinato cytochromes

2006 ◽  
Vol 62 (4) ◽  
pp. 1074-1087 ◽  
Author(s):  
Angelo Danilo Favia ◽  
Andrea Cavalli ◽  
Matteo Masetti ◽  
Angelo Carotti ◽  
Maurizio Recanatini
Keyword(s):  
Molecular Dynamics ◽  
Density Functional ◽  
Protoporphyrin Ix ◽  
Three Dimensional ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Human Aromatase

Three-dimensional model and molecular dynamics simulation of the active site of the self-splicing intervening sequence of the bacteriophage T4 nrdB messenger RNA

Biochemistry ◽  
1990 ◽  
Vol 29 (45) ◽  
pp. 10317-10322 ◽  
Author(s):  
Lennart Nilsson ◽  
Agneta Aahgren-Staalhandske ◽  
Ann Sofie Sjoegren ◽  
Solveig Hahne ◽  
Britt Marie Sjoeberg
Keyword(s):  
Molecular Dynamics ◽  
Active Site ◽  
Messenger Rna ◽  
Bacteriophage T4 ◽  
Three Dimensional ◽  
The Self ◽  
Dynamics Simulation ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Self Splicing

AFM-Based Nanoscratching: A 3D Molecular Dynamics Simulation With Experimental Verification

2014 ◽  
Author(s):  
Rapeepan Promyoo ◽  
Hazim El-Mounayri ◽  
Kody Varahramyan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Md Simulation ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Dimensional Model ◽  
Gold Substrate ◽  
Three Dimensional Model ◽  
Friction Forces ◽  
Defect Mechanism

In this paper, a developed three-dimensional model for AFM-based nanomachining is applied to study mechanical scratching at the nanoscale. The correlation between the scratching conditions, including applied force, scratching depth, and distant between any two scratched grooves, and the defect mechanism in the substrate/workpiece is investigated. The simulations of nanoscratching process are performed on different crystal orientations of single-crystal gold substrate, Au(100), Au(110), and Au(111). The material deformation and groove geometry are extracted from the final locations of atoms, which are displaced by the rigid indenter. The simulation also allows for the prediction of normal and friction forces at the interface between the indenter and substrate. An AFM is used to conduct actual scratching at the nanoscale, and provide measurements to which the MD simulation predictions are compared. The predicted forces obtained from MD simulation compares qualitatively with the experimental results.

Three-dimensional model of cytochrome P450 human aromatase

2005 ◽  
Vol 20 (6) ◽  
pp. 581-585 ◽  
Author(s):  
Cedric Loge ◽  
Marc Le Borgne ◽  
Pascal Marchand ◽  
Jean-Michel Robert ◽  
Guillaume Le Baut ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Three Dimensional ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Human Aromatase

The Intramolecular Hydrogen-Bond in Malonaldehyde as Seen by Infrared Spectroscopy. A Four-Dimensional Model Study

2003 ◽  
Vol 217 (12) ◽  
pp. 1507-1524 ◽  
Author(s):  
Nadja Došlić ◽  
O. Kühn
Keyword(s):  
Potential Energy ◽  
Density Functional ◽  
Three Dimensional ◽  
Deformation Mode ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Bending Vibrations ◽  
Functional Theory ◽  
Model Study ◽  
Intramolecular Hydrogen

AbstractThe infrared spectrum of the O–H–O fragment of malonaldehyde is studied using a four-dimensional model. This comprises the OH stretching and the two OH bending vibrations as well an O–O ring deformation mode under the assumption of overall Cs symmetry. The full anharmonic potential energy and dipole moment surfaces are calculated using density functional theory and the respective vibrational eigenvalue problem is solved by an iterative Lanczos method. Fundamental and combination transitions are discussed for the normal species and the symmetrically deuterated isotopomer. Special emphasis is paid to the OH/OD stretching region which reveals the signatures of strong mode mixing what renders a simple assignment in terms of fundamental transitions difficult. In addition results for hot transitions are presented which show a rather different OH/OD band due to the topology of the potential energy surface. The influence of H atom tunneling on the spectrum is briefly addressed employing an alternative three-dimensional model which takes into account the in-plane H atom motion as well as the O–O distance.

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