Molecular Dynamics Simulation of Zone Melting

1998 ◽  
Vol 09 (06) ◽  
pp. 857-860 ◽  
Author(s):  
P. Z. Coura ◽  
O. N. Mesquita ◽  
B. V. Costa
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Melting Process ◽  
Zone Melting ◽  
Dynamics Simulation

We use molecular dynamics technique for simulating the zone melting process. By tuning the parameters in the molecule–molecule potential we were able to reproduce segregation and fingering at the interface.

THE EFFECT OF THE RANGE OF THE POTENTIAL ON THE MULTI-STEP CLUSTER MELTING PROCESS

2004 ◽  
Vol 15 (05) ◽  
pp. 649-658 ◽  
Author(s):  
SHI-WEI REN
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Morse Potential ◽  
Melting Process ◽  
Dynamics Simulation ◽  
Repulsive Core ◽  
Tail Region ◽  
Step Process

By using the microcanonical molecular dynamics simulation, the melting processes of the clusters bound by Morse potential are investigated. It is found that these clusters show a multi-step melting process as long as the range of the Morse potential is a suitable value. The origins of this multi-step process are analyzed. I find that not only the repulsive core of the potential but also the attractive tail range of the potential influences the melting process. Moreover, the occurrence of the multi-step melting process is more sensitive to the tail region of the Morse potential.

Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study

2015 ◽  
Vol 93 (3) ◽  
pp. 348-361 ◽  
Author(s):  
C. Izanloo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Double Helix ◽  
Melting Process ◽  
Minor Groove ◽  
Dynamics Simulation ◽  
Transition Curve ◽  
Water Molecules ◽  
Major Groove ◽  
Dna Duplex

A molecular dynamics simulation was performed on a B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a saltwater medium with 1 mol/L NaCl concentration. The arrangements of water molecules and cations around the different atoms of DNA on the melting pathway were investigated. Almost for all atoms of the DNA by double helix → single-stranded transition, the water molecules released from the DNA duplex and cations were close to single-stranded DNA, but this behavior was not clearly seen at melting temperatures. Therefore, release of water molecules and cations approaching the DNA by the increase of temperature does not have any effect on the sharpness of the transition curve. Most of the water molecules and cations were found to be around the negatively charged phosphate oxygen atoms. The number of water molecules released from the first shell hydration upon melting in the minor groove was higher than in the major groove, and intrusion of cations into the minor groove after melting was higher than into the major groove. The hydrations of imino protons were different from each other and were dependent on DNA bases.

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