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.

scholarly journals How well do force fields capture the strength of salt bridges in proteins?

2018 ◽  
Author(s):  
Mustapha Carab Ahmed ◽  
Elena Papaleo ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Salt Bridge ◽  
Salt Bridges ◽  
Enhanced Sampling ◽  
Important Interaction ◽  
Close Proximity ◽  
The Stability ◽  
Dynamics Simulations

AbstractSalt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulations is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depend on the force field used. We have used NMR data on the B1 domain of protein G (GB1) to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is slightly overestimated in simulations of GB1 using six commonly used combinations of force fields and water models. We therefore conclude that further work is needed to refine our ability to model quantitatively the stability of salt bridges through simulations, and that comparisons between experiments and simulations will play a crucial role in furthering our understanding of this important interaction.

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