Spatial Redistribution of Niobium Additives Near Nickel Surfaces

1995 ◽  
Vol 408 ◽  
Author(s):  
Leonid S. Muratov ◽  
Bernard R. Cooper
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Harmonic Approximation ◽  
Lattice Relaxation ◽  
Pure Nickel ◽  
Quantum Mechanical ◽  
Concentration Limit ◽  
Vibrational Entropy ◽  
Quantum Mechanical Calculations ◽  
Spatial Redistribution

AbstractThe spatial redistribution of niobium atoms near the surface of pure nickel has been considered in the low niobium concentration limit. The calculation of free energy includes lattice relaxation around niobium atoms by using molecular dynamics (MD) incorporating atomistic potentials based on ab-initio quantum mechanical calculations and includes vibrational entropy phenomenologically within the local harmonic approximation.

scholarly journals Understanding the binding of inhibitors of matrix metalloproteinases by molecular docking, quantum mechanical calculations, molecular dynamics simulations, and a MMGBSA/MMBappl study

2015 ◽  
Vol 11 (4) ◽  
pp. 1041-1051 ◽  
Author(s):  
Tanya Singh ◽  
Olayiwola Adedotun Adekoya ◽  
B. Jayaram
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Matrix Metalloproteinases ◽  
Matrix Metalloproteinase ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Important Class ◽  
Matrix Metalloproteinase Inhibitors ◽  
Metalloproteinase Inhibitors ◽  
Dynamics Simulations

A computationally tractable pathway which helped in understanding the binding of matrix metalloproteinase inhibitors against an important class of MMPs is presented in this article.

scholarly journals A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243429
Author(s):  
Dimitrios A. Mitsikas ◽  
Nicholas M. Glykos
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Quantum Mechanical ◽  
Type I ◽  
Quantum Mechanical Calculations ◽  
Water Solvent ◽  
Simulation Protocol ◽  
Dynamics Simulations

Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 μs each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations within the DFT framework have shown that these peptides adopt β-turn structures in aqueous solution, with type I’ β-turn being the most preferred motif. The results from our analyses indicate that at least for the given systems, force field and simulation protocol, the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.

Molecular dynamics of ethisterone studied by 1H NMR, IINS and quantum mechanical calculations

2005 ◽  
Vol 317 (2-3) ◽  
pp. 178-187 ◽  
Author(s):  
Krystyna Holderna-Natkaniec ◽  
Kazimierz Jurga ◽  
Ireneusz Natkaniec ◽  
Dorota Nowak ◽  
Andrzej Szyczewski
Keyword(s):  
Molecular Dynamics ◽  
1H Nmr ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations
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