Dispersion curves from short-time molecular dynamics simulations. 1. Diatomic chain results

1988 ◽  
Vol 92 (12) ◽  
pp. 3386-3391 ◽  
Author(s):  
D. W. Noid ◽  
B. T. Broocks ◽  
S. K. Gray ◽  
S. L. Marple
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dispersion Curves ◽  
Diatomic Chain ◽  
Dynamics Simulations ◽  
Short Time

ANALYSIS OF THE MELTING PROCESS OF THE 14-PARTICLE MORSE CLUSTER THROUGH THE ATOMIC EQUIVALENCE INDEXES

2013 ◽  
Vol 27 (20) ◽  
pp. 1350142 ◽  
Author(s):  
SHI-WEI REN ◽  
YAN-ZHONG HAO
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Melting Process ◽  
Basic Structure ◽  
Cluster Exchange ◽  
Morse Clusters ◽  
Time Periods ◽  
Dynamics Simulations ◽  
Short Time

In this paper, by using the standard microcanonical molecular-dynamics simulations, the melting processes of the 14-particle Morse clusters are investigated. The three steps melting process found in 2004 by one of the authors of this paper are analyzed further by the atomic equivalence indexes. The properties of the structure of the cluster in different melting processes are explored by the atomic equivalence indexes. It is found that in the melting process for most of the time the cluster keeps the basic structure frame similar to that in the solid-like state while there are very short time periods when the particles of the cluster exchange their locations.

scholarly journals Confinement-induced self-organization in growing bacterial colonies

2021 ◽  
Vol 7 (4) ◽  
pp. eabc8685
Author(s):  
Zhihong You ◽  
Daniel J. G. Pearce ◽  
Luca Giomi
Keyword(s):  
Molecular Dynamics ◽  
Stress Relaxation ◽  
Molecular Dynamics Simulations ◽  
Mechanical Response ◽  
Self Organization ◽  
Global Alignment ◽  
Normal Stresses ◽  
Continuous Modeling ◽  
Dynamics Simulations ◽  
Short Time

We investigate the emergence of global alignment in colonies of dividing rod-shaped cells under confinement. Using molecular dynamics simulations and continuous modeling, we demonstrate that geometrical anisotropies in the confining environment give rise to an imbalance in the normal stresses, which, in turn, drives a collective rearrangement of the cells. This behavior crucially relies on the colony’s solid-like mechanical response at short time scales and can be recovered within the framework of active hydrodynamics upon modeling bacterial colonies as growing viscoelastic gels characterized by Maxwell-like stress relaxation.

scholarly journals Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations

2006 ◽  
Vol 5 (4) ◽  
pp. 1214-1226 ◽  
Author(s):  
John D. Chodera ◽  
William C. Swope ◽  
Jed W. Pitera ◽  
Ken A. Dill
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Molecular Dynamics Simulations ◽  
Folding Dynamics ◽  
Long Time ◽  
Dynamics Simulations ◽  
Short Time
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