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.

DEPENDENCE OF THE GLASS TRANSITION TEMPERATURE ON DENSITY IN A SOFT SPHERE SYSTEM WITH MORSE POTENTIAL

2002 ◽  
Vol 16 (18) ◽  
pp. 669-675
Author(s):  
HAO-YANG LIU ◽  
WEN-BING ZHANG ◽  
XIAN-WU ZOU ◽  
YIN-QUAN YUAN ◽  
ZHUN-ZHI JIN
Keyword(s):  
Molecular Dynamics ◽  
Glass Transition ◽  
Transition Temperature ◽  
Glass Transition Temperature ◽  
Molecular Dynamics Simulation ◽  
Partition Function ◽  
Morse Potential ◽  
Function Analysis ◽  
Dynamics Simulation ◽  
Soft Sphere

The glass transition for the soft sphere system with Morse potential was investigated based on molecular dynamics simulation and partition function analysis. The dependence of the glass transition temperature on the density and the softness of the potential was obtained.

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.

Calculation of Material Properties Using Molecular Dynamics Simulation

2007 ◽  
Author(s):  
Y. H. Park ◽  
J. Tang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Melting Point ◽  
Material Properties ◽  
Morse Potential ◽  
Formation Energy ◽  
Dynamics Simulation ◽  
Embedded Atom Method ◽  
Embedded Atom ◽  
Dynamics Method

This paper describes the calculation of material properties of copper (Cu) using the molecular dynamics method. Vacancy formation energy, bulk modulus, surface energy and melting point are calculated using different potentials such as the Morse potential and Embedded Atom Method (EAM). Results obtained from different potentials are discussed and compared with experimental results.

scholarly journals Complexation of 26-Mer Amylose with Egg Yolk Lipids with Different Numbers of Tails Using a Molecular Dynamics Simulation

Foods ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2355
Author(s):  
Shangyuan Sang ◽  
Xueming Xu ◽  
Xiao Zhu ◽  
Ganesan Narsimhan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Egg Yolk ◽  
Dynamics Simulation ◽  
Helical Conformation ◽  
Stable Complex ◽  
Tail Region ◽  
Cross Sectional ◽  
Average Binding Energy ◽  
Helical Region

A molecular dynamics simulation of mixtures of 26-mer amylose with three different egg yolk lipids, namely, cholesterol, triglyceride and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), demonstrated the formation of a stable complex. The 26-mer amylose fluctuated between a coiled and an extended helical conformation. The complex was a V-type amylose complex, with the hydrophobic tail of the lipids being inside the hydrophobic helical cavity of the amylose. The number of glucose units per turn was six for the two helical regions of the amylose-POPC complex and the palmitoyl tail region of the amylose-triglyceride complex. This value was eight for the cholesterol and the two-tail helical region in the amylose-triglyceride complex. Two tails of the POPC were in two different hydrophobic helical regions of the 26-mer amylose, whereas the palmitoyl tail of the triglyceride lay in one hydrophobic helical region and the linoleoyl and oleoyl tails both lay in another helical region, and the cross-sectional area of the latter was larger than the former to accommodate the two tails. The radii of the gyration of the complex were lower for all three cases compared to that of one single amylose. In addition, the stability of the complexes was ranked in the following order: POPC < cholesterol < triglyceride, with their average binding energy being −97.83, −134.09, and −198.35 kJ/mol, respectively.

Molecular Dynamics Simulation Study of Grinding Process of Mg-Al Alloy

2013 ◽  
Vol 820 ◽  
pp. 75-79 ◽  
Author(s):  
Cai Xia Li ◽  
Yu Luo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Morse Potential ◽  
Cutting Speed ◽  
Dynamics Simulation ◽  
Depth Of Cut ◽  
Al Alloy ◽  
Grinding Process ◽  
Embedded Atom ◽  
Eam Potential

A molecular dynamics simulation considered of chip deformation and force analysis for grinding process of Mg-Al alloy is presented. Hybrid potentials including embedded atom method (EAM) potential and Morse potential are applied in this model. The activities among atoms of Mg-Al Alloy material is described by EAM potential which is very suitable for metal materials. Morse potential is used to realize the interaction between Mg-Al alloy and abrasive grain made of diamond. Simulations of Different depths of cut (0.6nm, 0.8nm and 1.0nm) and different cut speeds (50m/s, 100m/s and 200m/s) are given. The experience result shows that with the same nanometric depth of cut, there is a little difference of ratio of the cut potential to the cutting speed. Moreover, with the same cutting speed, the cut potential is increased linearly with the depth of cut while reaching to stable cutting regime.

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