scholarly journals Investigation of the Effects of N-Linked Glycans on the Stability of the Spike Protein in SARS-CoV-2 by Molecular Dynamics Simulations

2022 ◽  
Author(s):  
Emine Deniz Tekin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Local Stability ◽  
Spike Protein ◽  
Spike Glycoprotein ◽  
Full Structure ◽  
The Stability ◽  
Dynamics Simulations ◽  
Spike Proteins

We perform all-atom molecular dynamics simulations to study the effects of the N-linked glycans on the stability of the spike glycoprotein in SARS-CoV-2. After a 100 ns of simulation on the spike proteins without and with the N-linked glycans, we found that the presence of glycans increases the local stability in their vicinity; even though their effect on the full structure is negligible.

New molecular insights into the stability of Ni–Pd hollow nanoparticles

2017 ◽  
Vol 4 (10) ◽  
pp. 1679-1690 ◽  
Author(s):  
Hamed Akbarzadeh ◽  
Esmat Mehrjouei ◽  
Amir Nasser Shamkhali ◽  
Mohsen Abbaspour ◽  
Sirous Salemi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Behavior ◽  
Molecular Dynamics Simulations ◽  
Structural Evolution ◽  
Hollow Nanoparticles ◽  
The Stability ◽  
Dynamics Simulations

Molecular dynamics simulations were used to investigate the structural evolution and thermal behavior of Ni–Pd hollow nanoparticles.

scholarly journals Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures

1999 ◽  
Vol 8 (6) ◽  
pp. 1292-1304 ◽  
Author(s):  
Lu Wang ◽  
Yong Duan ◽  
Rebecca Shortle ◽  
Barbara Imperiali ◽  
Peter A. Kollman
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Different Temperatures ◽  
The Stability ◽  
Dynamics Simulations

MOLECULAR DYNAMICS SIMULATIONS OF CARBON NANOTUBE-BASED OSCILLATORS HAVING TOPOLOGICAL DEFECTS

2011 ◽  
Vol 10 (01n02) ◽  
pp. 355-359 ◽  
Author(s):  
MATUKUMILLI. V. D. PRASAD ◽  
BAIDURYA BHATTACHARYA
Keyword(s):  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulations ◽  
Topological Defects ◽  
Oscillatory Behavior ◽  
Vacancy Defect ◽  
Single Vacancy ◽  
Vacancy Defects ◽  
The Stability ◽  
Dynamics Simulations

Effect of vacancy and Stone–Wales defects on the oscillatory behavior of (5,5)/(10,10) carbon nanotube-based oscillator are studied using NVE molecular dynamics simulations. Results show that defects reduce stability of the oscillators. Effect of single vacancy defect on stability is very small, whereas Stone–Wales defect considerably reduces the stability thereby damping the oscillations quickly. Further increase in density of vacancy defects causes a monotonic decrease of stability of oscillator. In all cases the initial temperature (1 and 300 K) had almost no effect on the oscillation stability.

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