On the thermal stability of tetrahedrane: Tight-binding molecular dynamics study

2011 ◽  
Vol 387 (1-3) ◽  
pp. 66-68 ◽  
Author(s):  
Mikhail M. Maslov ◽  
Konstantin P. Katin
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Tight Binding ◽  
Thermal Stability Of

Simulation of Thermal Stability and Friction: A Lubricant Confined Between Monolayers of Wear Inhibitors on Iron Oxide

1998 ◽  
Vol 543 ◽  
Author(s):  
T. Çağin ◽  
Y. Zhou ◽  
E. S. Yamaguchi ◽  
R. Frazier ◽  
A. Ho ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Quantum Chemical ◽  
Md Simulations ◽  
Atomic Level ◽  
The Self ◽  
Self Assembled Monolayer ◽  
Thermal Stabilities ◽  
Frictional Forces ◽  
Thermal Stability Of

AbstractTo understand antiwear phenomena in motor engines at the atomic level and provide evidence inselecting future ashless wear inhibitors, we studied the thermal stability of the self-assembled monolayer(SAM) model for dithiophosphate (DTP) and dithiocarbamate (DTC) molecules on the iron oxidesurface using molecular dynamics. The interactions for DTP, DTC and Fe2O3 are evaluated based on aforce field derived from fitting to ab initio quantum chemical calculations of dimethyl DTP (and DTC)and Fe(OH)2(H2O)2-DTP (DTC) clusters. MD simulations at constant-NPT are conducted to assesrelative thermal stabilities of the DTP and DTC with different pendant groups (n-propyl, i-propyl, npentyl.and i-pentyl). To investigate frictional process, we employ a steady state MD method, in whichone of the Fe2O3 slabs maintained at a constant linear velocity. We obtain the time averaged normaland frictional forces from the interatomic forces. Then, we calculated the friction coefficient at theinterface between SAMs of DTP and the confined lubricant, hexadecane, to assess the shear stability ofDTPs with different pendant groups.

scholarly journals A Possible Mechanism of Graphene Oxide to Enhance Thermostability of D-Psicose 3-Epimerase Revealed by Molecular Dynamics Simulations

2021 ◽  
Vol 22 (19) ◽  
pp. 10813
Author(s):  
Congcong Li ◽  
Zhongkui Lu ◽  
Min Wang ◽  
Siao Chen ◽  
Lu Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Graphene Oxide ◽  
Md Simulations ◽  
Strong Interactions ◽  
Limiting Factor ◽  
Active Site Residues ◽  
Detailed Mechanism ◽  
Dynamics Simulations ◽  
Thermal Stability Of

Thermal stability is a limiting factor for effective application of D-psicose 3-epimerase (DPEase) enzyme. Recently, it was reported that the thermal stability of DPEase was improved by immobilizing enzymes on graphene oxide (GO) nanoparticles. However, the detailed mechanism is not known. In this study, we investigated interaction details between GO and DPEase by performing molecular dynamics (MD) simulations. The results indicated that the domain (K248 to D268) of DPEase was an important anchor for immobilizing DPEase on GO surface. Moreover, the strong interactions between DPEase and GO can prevent loop α1′-α1 and β4-α4 of DPEase from the drastic fluctuation. Since these two loops contained active site residues, the geometry of the active pocket of the enzyme remained stable at high temperature after the DPEase was immobilized by GO, which facilitated efficient catalytic activity of the enzyme. Our research provided a detailed mechanism for the interaction between GO and DPEase at the nano–biology interface.

Thermal stability of zirconia-doped ceria surfaces: A first-principles molecular dynamics study

2020 ◽  
Vol 507 ◽  
pp. 144942
Author(s):  
Gege Zhou ◽  
Wen-Tong Geng ◽  
Wei Xiao ◽  
Lu Sun ◽  
Jianwei Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
First Principles ◽  
Doped Ceria ◽  
Thermal Stability Of ◽  
First Principles Molecular Dynamics

scholarly journals A study of the structural properties and thermal stability of human Bcl-2 by molecular dynamics simulations

2013 ◽  
Vol 32 (11) ◽  
pp. 1707-1719 ◽  
Author(s):  
Ian Ilizaliturri-Flores ◽  
José Correa-Basurto ◽  
Claudia G. Benítez-Cardoza ◽  
Absalom Zamorano-Carrillo
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Molecular Dynamics Simulations ◽  
Structural Properties ◽  
Dynamics Simulations ◽  
Thermal Stability Of

scholarly journals Molecular Dynamics Simulation of Barnase: Contribution of Noncovalent Intramolecular Interaction to Thermostability

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Zhiguo Chen ◽  
Yi Fu ◽  
Wenbo Xu ◽  
Ming Li
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Molecular Dynamics Simulation ◽  
Root Mean Square ◽  
Clinical Medicine ◽  
Intramolecular Interaction ◽  
Salt Bridge ◽  
Dynamics Simulation ◽  
Mean Square ◽  
Thermal Stability Of

Bacillus amyloliquefaciensribonuclease Barnase (RNase Ba) is a 12 kD (kilodalton) small extracellular ribonuclease. It has broad application prospects in agriculture, clinical medicine, pharmaceutical, and so forth. In this work, the thermal stability of Barnase has been studied using molecular dynamics simulation at different temperatures. The present study focuses on the contribution of noncovalent intramolecular interaction to protein stability and how they affect the thermal stability of the enzyme. Profiles of root mean square deviation and root mean square fluctuation identify thermostable and thermosensitive regions of Barnase. Analyses of trajectories in terms of secondary structure content, intramolecular hydrogen bonds and salt bridge interactions indicate distinct differences in different temperature simulations. In the simulations, Four three-member salt bridge networks (Asp8-Arg110-Asp12, Arg83-Asp75-Arg87, Lys66-Asp93-Arg69, and Asp54-Lys27-Glu73) have been identified as critical salt bridges for thermostability which are maintained stably at higher temperature enhancing stability of three hydrophobic cores. The study may help enlighten our knowledge of protein structural properties, noncovalent interactions which can stabilize secondary peptide structures or promote folding, and also help understand their actions better. Such an understanding is required for designing efficient enzymes with characteristics for particular applications at desired working temperatures.

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