Molecular Dynamics Simulations on the Chain Fold During the Isothermal Orientation of n-Alkanes on Graphene

2021 ◽  
Author(s):  
Zhi Meng Zhang ◽  
Hua Yang ◽  
Jun Xia Shi ◽  
Jia Jun Wang ◽  
Zheng Guo Huang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Orientation ◽  
Dynamics Simulation ◽  
Ordered Structure ◽  
Graphene Surface ◽  
Parallel Orientation ◽  
Chain Folding ◽  
Hydrocarbon Chains ◽  
Simulation Results ◽  
Dynamics Simulations

Abstract The orientation of hydrocarbon chains plays a key role in the applications of organic materials. And chain folding in the process of molecular orientation is also of great significance for the design of organic molecular thin films. The effect of chain length and simulation temperature on the isothermal orientation of n-alkanes on graphene surface is studied by molecular dynamics simulation in this paper. And the chain folding is also described. The n-alkanes can form perpendicular ordered structure, parallel ordered structure or perpendicular orientation at relative low temperature and parallel orientation at relative high temperature on graphene surface. The chain fold happens when long n-alkanes form perpendicular ordered structure on graphene surface. And the simulation results show the interactions of n-alkane−graphene and n-alkane−n-alkane affect chain fold.

Molecular Dynamics Simulation Study of Lecithin Inhibiting Hydrate-Dissociation

2017 ◽  
Vol 890 ◽  
pp. 252-259
Author(s):  
Le Wang ◽  
Guan Cheng Jiang ◽  
Xin Lin ◽  
Xian Min Zhang ◽  
Qi Hui Jiang
Keyword(s):  
Molecular Dynamics ◽  
Water Movement ◽  
Simulation Analysis ◽  
Mass Density ◽  
Dynamics Simulation ◽  
Dissociation Process ◽  
Hydrate Dissociation ◽  
Hydrocarbon Chains ◽  
Dynamics Simulations ◽  
Mass Density Profile

Molecular dynamics simulations are used to study the dissociation inhibiting mechanism of lecithin for structure I hydrates. Adsorption characteristics of lecithin and PVP (poly (N-vinylpyrrolidine)) on the hydrate surfaces were performed in the NVT ensemble at temperatures of 277K and the hydrate dissociation process were simulated in the NPT ensemble at same temperature. The results show that hydrate surfaces with lecithin is more stable than the ones with PVP for the lower potential energy. The conformation of lecithin changes constantly after the balanced state is reached while the PVP molecular dose not. Lecithin molecule has interaction with lecithin nearby and hydrocarbon-chains of lecithin molecules will form a network to prevent the diffusion of water and methane molecules, which will narrow the available space for hydrate methane and water movement. Compared with PVP-hydrate simulation, analysis results (snapshots and mass density profile) of the dissociation simulations show that lecithin-hydrate dissociates more slowly.

Molecular Dynamics Simulations of Nanocomposite Diamond-Like Carbon

2005 ◽  
Author(s):  
G. T. Gao ◽  
J. D. Schall ◽  
K. Van Workum ◽  
P. T. Mikulski ◽  
J. A. Harrison
Keyword(s):  
Molecular Dynamics ◽  
Elastic Constants ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Diamond Structure ◽  
The Core ◽  
Constant Tension ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Carbon Network

A constant tension and constant temperature molecular dynamics simulation method was used in the calculations of the elastic constants of the nanocomposite systems. The nanocomposite systems contain a core of sp3 diamond structure surrounded by an amorphous carbon network. The simulation results show that the elastic properties of nanocomposites of diamond-like carbons are closely related to the size of the sp3 diamond core; the bigger the core, the larger the elastic constants, and the system becomes more anisotropic.

Molecular dynamics simulation of a hydrated phospholipid bilayer

1994 ◽  
Vol 344 (1309) ◽  
pp. 239-260 ◽  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Complex Systems ◽  
Phospholipid Bilayer ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Hydrocarbon Chains ◽  
Membrane Bound ◽  
Simulation Results ◽  
Well Data

A hydrated bilayer of the phospholipid 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) has been studied in the course of a molecular dynamics simulation. Comparison of the simulation results with experiment indicates that generally the two agree well. Data are presented concerning all the major system regions, including the hydrocarbon chains, the glycerol region, the lipid headgroups and the hydrating water molecules. The simulations suggest that this model can be extended to the study of more complex systems of greater biochemical interest, such as membrane bound proteins.

Thermal Conductivity of Silicon Thin Films Predicted by Molecular Dynamics Simulations and Theoretical Calculation

2011 ◽  
Vol 55-57 ◽  
pp. 1152-1155 ◽  
Author(s):  
Xing Li Zhang ◽  
Zhao Wei Sun
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Boltzmann Transport Equation ◽  
Phonon Transport ◽  
Dynamics Simulation ◽  
Boltzmann Transport ◽  
Silicon Thin Films ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Good Agreement

Molecular, dynamics simulation and the Boltzmann transport equation are used respectively to analyze the phonon transport in Si thin film. The MD result is in good agreement with the theoretical analysis values. The results show that the calculated thermal conductivity decreases almost linearly as the film thickness reduced and is almost independent of the temperature at the nanoscale. It was observed from the simulation results that there exists the obvious size effect on the thermal conductivity.

Frictional Characteristics of Graphene Layers Using Molecular Dynamics Simulation

NANO ◽  
2016 ◽  
Vol 11 (09) ◽  
pp. 1650096 ◽  
Author(s):  
Te-Hua Fang ◽  
Win-Jin Chang ◽  
Fu-Yung Tung
Keyword(s):  
Molecular Dynamics ◽  
Dynamics Simulation ◽  
Stick Slip ◽  
Scanning Velocity ◽  
Graphene Surface ◽  
Graphene Layers ◽  
Atomic Force ◽  
Afm Probe ◽  
Lower Temperature ◽  
Dynamics Simulations

Molecular dynamics simulations of an atomic force microscope (AFM) probe scanning the surface of a five-layer graphene were conducted. The AFM-like scanning probe was modeled by a capped single-wall carbon nanotube. Note that interference with the graphene surface induced frictional behavior; moreover, the effects on the friction system of scanning velocity, probe direction and temperature were investigated. Wrinkling of the graphene surface became more apparent at higher temperatures, while stick-slip friction was more apparent at a lower temperature and a slower scanning velocity. The friction coefficient of the system was approximately 0.001.

Evaluation of Thermal Rectification at the Interface of Double-Layered Nanofilm by Molecular Dynamics Simulations

2008 ◽  
Author(s):  
Juekuan Yang ◽  
Zhenghua Liu ◽  
Yujuan Wang ◽  
Yunfei Chen
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Thermal Resistance ◽  
Dynamics Simulation ◽  
Interfacial Thermal Resistance ◽  
Thermal Rectification ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Increasing Temperature

The thermal rectification at the interface of double-layered nanofilm is investigated by molecular dynamics simulation. It is found that the interfacial thermal resistance is asymmetric, namely, it depends on the direction of heat flow across the interface. And at high temperature, the rectification of interfacial thermal resistance decreases with increasing temperature. The simulation results also demonstrated that the rectifying effects can not be interpreted only by temperature difference at interface.

scholarly journals Recrystallization and size distribution of dislocated segments in cellulose microfibrils—a molecular dynamics perspective

Cellulose ◽  
2021 ◽  
Author(s):  
Ali Khodayari ◽  
Ulrich Hirn ◽  
Stefan Spirk ◽  
Aart W. Van Vuure ◽  
David Seveno
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Crystalline State ◽  
Analytical Data ◽  
Dynamics Simulation ◽  
Cellulose Microfibrils ◽  
Acid Vapor ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Hydrolysis Of

Abstract The arrangement of cellulose molecules in natural environment on the nanoscale is still not fully resolved, with longitudinal disorder in cellulose microfibrils (CMF) being one relevant question. Particularly the length of the dislocated cellulose segments in CMFs is still under debate. Using molecular dynamics simulations, we are first investigating the phenomenon of pseudo-recrystallization of dislocated cellulose regions after cleavage of CMFs. Based on our simulations we propose that 3–4 glucose residues bordering to each side of a cellulose nanocrystal are actually reorganizing to a quasi-crystalline state, which are corroborating recent analytical investigations reporting an increase in crystallinity after acid vapor hydrolysis of CMFs. Combining our molecular dynamics simulation results with these analytical data we can estimate the length of the dislocated cellulose segments in CMFs. We propose that, for the investigated sources of biomass (cotton and ramie), the dislocation lengths are between 3.1–5.8 nm equaling to 6–11 glucose residues in the cellulose crystallites. Graphic abstract

scholarly journals Molecular Dynamics Simulation of Chain Folding for Polyethylene Subjected to Vibration Excitation

2014 ◽  
Vol 2014 ◽  
pp. 1-9
Author(s):  
Junfeng Gu ◽  
Xue Wang ◽  
Jinying Wu ◽  
Xicheng Wang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Periodic Force ◽  
Chain Folding ◽  
Vibration Effect ◽  
Vibration Excitation ◽  
Folding Simulation ◽  
Simulation Results ◽  
Dynamics Method

We propose a molecular dynamics method with vibration excitation, named as VEMD, to investigate the vibration effect on chain folding for polymer molecule. The VEMD method is based on the introduction of periodic force, the amplitude and frequency of which can be adjusted, and the method was applied to the folding simulation of a polyethylene chain. Simulation results show that the vibration excitation significantly affects the folding of the polyethylene, and frequency and amplitude of the vibration excitation play key roles in VEMD. Different frequencies and amplitudes will determine how and to what extent does the vibration excitation affect the folding process of the polyethylene structure.

The Study of Argon’s Viscosity Near the Wall of Nanopore by Molecular Dynamics Simulations

2013 ◽  
Author(s):  
Qixin Liu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Gas Flow ◽  
Molecular Motion ◽  
Dynamics Simulation ◽  
Wall Surface ◽  
Number Density ◽  
Flow Phenomena ◽  
Simulation Results ◽  
Dynamics Simulations

Many uncommon gas flow phenomena in nanopores have been found by experiments. Besides that, another special characteristic of gas flow at nanopore is that gas’s number density shows uneven distribution. From the point of molecular motion, gas’s number density would affect its dynamic viscosity, so it’s very necessary to study whether the gas’s viscosity is uneven. Due to the gas density’s fluctuation usually takes place near the wall surface so the present paper focuses on the gas’s viscosity near the wall of nanopore. Our molecular dynamics simulation results indicate that the gas’s viscosity in the region near the wall surface isn’t a constant and fluctuates greatly. The profiles of gas’s viscosity and gas number density coincide very well.

Molecular Dynamics Simulation of ZnO Nanowire Manipulation

2014 ◽  
Vol 609-610 ◽  
pp. 400-405
Author(s):  
Dong Jie Li ◽  
Li Zhang ◽  
Jian Song
Keyword(s):  
Molecular Dynamics ◽  
Optimal Operation ◽  
Dynamics Simulation ◽  
Force Model ◽  
Zno Nanowire ◽  
Transfer Experiment ◽  
Zno Nanostructure ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Substrate Model

In order to achieve a better manipulation performance of ZnO nanowire, the ZnO nanowire forces are analysed, and molecular dynamics simulations are conducted. Force model of ZnO nanowire is established to interprete the drifting, bending and fracturing conditions in ZnO nanowire transfer experiment. As ZnO nanowire force is too complex to build a precise mathematical model, molecular dynamics is proposed to simulate the process. Based on the analysis of ZnO nanostructure, the probe-nanowire-substrate model is established. Through changing the operation path of the probe and operation area between the probe and nanowire, simulation results are got. By the Analysis and comparison of simulation results, the optimal operation path and operation area are obtained.

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