Dynamic Specification of Initial Structures in Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Efficiently Promotes Biologically Relevant Rare Events

2017 ◽  
Vol 90 (11) ◽  
pp. 1236-1243 ◽  
Author(s):  
Ryuhei Harada ◽  
Yasuteru Shigeta
Keyword(s):  
Molecular Dynamics ◽  
Rare Events ◽  
Biologically Relevant ◽  
Dynamic Specification

Structural relaxation in Ag-Ni nanoparticles: Atomistic modeling away from equilibrium

2021 ◽  
Author(s):  
Florent Calvo
Keyword(s):  
Molecular Dynamics ◽  
Structural Relaxation ◽  
Rare Events ◽  
Metal Vapor ◽  
Silver Concentration ◽  
Atomistic Modeling ◽  
Ni Nanoparticles ◽  
Vapor Mixture ◽  
Chemical Ordering ◽  
Fast Cooling

The out-of-equilibrium structural relaxation of Ag-Ni nanoparticles containing about 1000--3000 atoms was investigated computationally by means of molecular dynamics trajectories in which the temperature is decreased gradually over hundreds of nanoseconds. At low silver concentration of 10--30\%, the evolution of chemical ordering in Ni$_{\rm core}$Ag$_{\rm shell}$ nanoparticles with different surface arrangements is found to proceed spontaneously and induce some rounding of the nickel core and its partial recristallization. Fast cooling of an initially hot metal vapor mixture was also considered, and it is shown to disfavor silver aggregation at the surface. Silver impurities are also occasionally produced but remain rare events under the conditions of our simulations.

Accelerating rare events using temperature programmed molecular dynamics: a review

2019 ◽  
Vol 45 (14-15) ◽  
pp. 1295-1303
Author(s):  
Saurabh Shivpuje ◽  
Methary Jaipal ◽  
Abhijit Chatterjee
Keyword(s):  
Molecular Dynamics ◽  
Rare Events ◽  
Temperature Programmed

scholarly journals The Integrin Receptor in Biologically Relevant Bilayers: Insights from Molecular Dynamics Simulations

2016 ◽  
Vol 250 (4) ◽  
pp. 337-351 ◽  
Author(s):  
Antreas C. Kalli ◽  
Tomasz Rog ◽  
Ilpo Vattulainen ◽  
Iain D. Campbell ◽  
Mark S. P. Sansom
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Integrin Receptor ◽  
Biologically Relevant ◽  
Dynamics Simulations

scholarly journals Action-Derived Molecular Dynamics in the Study of Rare Events

2001 ◽  
Vol 87 (10) ◽  
Author(s):  
Daniele Passerone ◽  
Michele Parrinello
Keyword(s):  
Molecular Dynamics ◽  
Rare Events

scholarly journals Characterization of Rare Events in Molecular Dynamics

Entropy ◽  
2013 ◽  
Vol 16 (1) ◽  
pp. 350-376 ◽  
Author(s):  
Carsten Hartmann ◽  
Ralf Banisch ◽  
Marco Sarich ◽  
Tomasz Badowski ◽  
Christof Schütte
Keyword(s):  
Molecular Dynamics ◽  
Rare Events
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