Alanine Polypeptide Structural Fingerprints at Room Temperature: What Can Be Gained from Non-Harmonic Car−Parrinello Molecular Dynamics Simulations

2008 ◽  
Vol 112 (51) ◽  
pp. 13507-13517 ◽  
Author(s):  
M.-P. Gaigeot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Room Temperature ◽  
Dynamics Simulations

When do defectless alkanethiol SAMs in ionic liquids become penetrable? A molecular dynamics study

2015 ◽  
Vol 17 (47) ◽  
pp. 31947-31955 ◽  
Author(s):  
Sergey A. Kislenko ◽  
Victoria A. Nikitina ◽  
Renat R. Nazmutdinov
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulations ◽  
Room Temperature ◽  
Room Temperature Ionic Liquid ◽  
Self Assembled Monolayers ◽  
Assembled Monolayers ◽  
Self Assembled ◽  
Dynamics Simulations

Molecular dynamics simulations were performed to address the permeability of defectless alkanethiol self-assembled monolayers (SAMs) on charged and uncharged Au(111) surfaces in 1-butyl-3-methylimidazolium ([bmim][BF4]) room-temperature ionic liquid (IL).

scholarly journals Ammonium based stabilizers effectively counteract urea-induced denaturation in a small protein: insights from molecular dynamics simulations

RSC Advances ◽  
2017 ◽  
Vol 7 (83) ◽  
pp. 52888-52906 ◽  
Author(s):  
Soham Sarkar ◽  
Soumadwip Ghosh ◽  
Rajarshi Chakrabarti
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Room Temperature ◽  
Conformational Stability ◽  
Deep Eutectic Solvents ◽  
Room Temperature Ionic Liquids ◽  
Small Protein ◽  
Dynamics Simulations

Room temperature ionic liquids (IL) and deep eutectic solvents (DES) are known to aid the conformational stability and activity of proteins and enzymes in aqueous solutions.

scholarly journals Nitrogenation of Amorphous Silicon : Reactive Molecular Dynamics Simulations

2019 ◽  
Vol 8 (3) ◽  
pp. 197-207
Author(s):  
Mauludi Ariesto Pamungkas ◽  
◽  
Choirun Nisa ◽  
Istiroyah Istiroyah ◽  
Abdurrouf Abdurrouf ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Silicon Nitride ◽  
Nitrogen Atom ◽  
Molecular Dynamics Simulations ◽  
Room Temperature ◽  
Crystalline Silicon ◽  
Semiconductor Industry ◽  
Reactive Force ◽  
Reactive Molecular Dynamics ◽  
Dynamics Simulations

Since silicon nitride (SiNx) film is more stable than SiO2, silicon nitride, thus it is widely used in semiconductor industry as an insulatorlayer. The study of nitrogenation process of a-Si was performed using molecular dynamics simulations to determine the properties of the bonds created in the structure of a-SiNx. Reactive force field (Reaxff) was used as potential in this molecular dynamic simulation owing to its ability to describe charge transfer as well as breaking and formation of atomic bonds. The structure of a-Si is obtained by melting the crystalline silicon at temperature of 3500 K followed by quenching to room temperature. The nitrogenation process was carried out by randomly distributing 900 N atoms over the a-Si surface for 60 ps at temperature varied from 300 K, 600 K, 900 K, and 1200 K. The higher the temperature nitrogenation applied in the system, the more number of N atoms adsorbed, resulting in a deeper penetration depth of Nitrogen atom. Amorphization and nitrogenation changed the distribution of coordination number of Ni, Si, and O atoms. Transfer of electrons from silicon to nitrogen occurs only in the nearest nitrogen atom with silicon atom.

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