Molecular Dynamics Simulation of Water-Based Nano-Lubrication

2013 ◽  
Vol 773 ◽  
pp. 585-588
Author(s):  
Su Mei Zhang ◽  
Pei Hong Guo ◽  
Jia Nan Zhu ◽  
Xiao Ping Wen
Keyword(s):  
Molecular Dynamics ◽  
Reduction Rate ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Stabilization Time ◽  
Shear Rates ◽  
Water Based ◽  
Dynamics Simulations ◽  
Metal Wall ◽  
Number Of Particles

Molecular dynamics simulations of water-based nanolubrication in Couette flow are carried out. The water molecules are simulated by the TIP3P model. Three different shear rates are 20 m/s and 40 m/s and 60 m/s, and the vertical pressure acted on the metal wall are 10GPa, 20 GPa, 30 GPa and 40 GPa respectively. The simulated results show that the greater pressure, the smaller the stable value of friction spacing, while the reduction rate of the stable value becomes small. Meanwhile, as pressure increases, the stabilization time is longer. However, under the same pressure, shear rate of influence on the friction spacing is not obvious. The friction spacing increases with the number of particles, showing that the presence of nanoparticles can enhance the bearing capacity.

Acceleration of molecular dynamics simulation of multiphase systems on GPU

2012 ◽  
Vol 9 (2) ◽  
pp. 76-79
Author(s):  
D.F. Marin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Intermolecular Interaction ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Lennard Jones ◽  
Multiphase Systems ◽  
And Performance ◽  
Dynamics Simulations

The paper presents results on acceleration of molecular dynamics simulations with the usage of GPUs. A system of water molecules is considered as an example of polar liquid. The intermolecular interaction is modeled with the usage of Coulomb and truncated Lennard-Jones potentials. Results of computational experiments on acceleration and performance of the developed code are presented.

scholarly journals Transport mechanisms of water molecules and ions in sub-nano channels of nanostructured water treatment liquid-crystalline membranes: a molecular dynamics simulation study

2020 ◽  
Vol 6 (3) ◽  
pp. 604-611 ◽  
Author(s):  
Hiroki Nada ◽  
Takeshi Sakamoto ◽  
Masahiro Henmi ◽  
Takafumi Ogawa ◽  
Masahiro Kimura ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Water Treatment ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Liquid Crystalline ◽  
Dynamics Simulation ◽  
Self Organization ◽  
Water Molecules ◽  
Transport Mechanisms ◽  
Dynamics Simulations

Transport mechanisms of water molecules and ions in the liquid crystalline (LC) membranes with sub-nano channels formed by self-organization of thermotropic ionic LC compounds were elucidated by molecular dynamics simulations.

Molecular Dynamics Simulation of Quasi-Two-Dimensional Water Network on Ice Nucleation Protein

2011 ◽  
Author(s):  
Daisuke Murakami ◽  
Kenji Yasuoka
Keyword(s):  
Molecular Dynamics ◽  
Water Clusters ◽  
Ice Nucleation ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Two Dimensional ◽  
Threshold Density ◽  
Ice Nucleation Protein ◽  
Network Of Hydrogen Bonds ◽  
Dynamics Simulations

An ice nucleation protein induces a phase transition from liquid water to ice in air. A specific hydrophilic surface of the protein may have an influence on the network of hydrogen bonds touching on the protein. However, microscopic characteristics of the ice nucleation protein and behavior of water molecules on it have not been clarified. So we carried out molecular dynamics simulations in various quasi-two-dimensional densities of water molecules on the ice nucleation protein. The percolation threshold of water clusters was confirmed. Comparing another hydrophilic protein, the threshold density in both cases had nearly the same value. But percolation probabilities and mean cluster sizes near the threshold were different between both cases. Those results implied that the threshold density was consistent with the conventional theory, but the forming of water clusters near the threshold was influenced by the hydrophilicity on the ice nucleation protein.

scholarly journals A method for detection of permeation events in Molecular Dynamics simulations of lipid bilayers

2021 ◽  
Author(s):  
Carlos R. S. Camilo ◽  
J. Roberto Ruggiero ◽  
Alexandre S. de Araujo
Keyword(s):  
Molecular Dynamics ◽  
Cell Membrane ◽  
Lipid Bilayers ◽  
Complex Structure ◽  
Phospholipid Bilayer ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Human Knowledge ◽  
Crossing Time ◽  
Dynamics Simulations

The cell membrane is one of the most important structures of life. Understanding its functioning is essential for several human knowledge areas, mainly how it controls the efflux of substances between the cytoplasm and the environment. Being a complex structure, composed of several classes of compounds such as lipids, proteins, sugars, etc., a convenient way to mimic it is through a phospholipid bilayer. The Molecular Dynamics simulation of lipid bilayers in solution is the main computational approach to model the cell membrane. In this work, we present a method to detect permeation events of molecules through the lipid bilayer, characterizing its crossing time and trajectory. By splitting the simulation box into well-defined regions, the method distinguishes the passage of molecules through the bilayer from artifacts produced by crossing molecules through the simulation box edges when using periodic boundary conditions. We apply the method to study the spontaneous permeation of water molecules through bilayers with different lipid compositions and modeled with different force fields. Our method successfully characterizes the permeation events, and the results obtained show that the frequency and time of permeation are independent of the force field used to model the phospholipids. Besides, it is observed that the increase in the concentration of cholesterol molecules in lipid bilayers induces the reduction of permeation events due to its compacting action on the bilayer, making it denser and, therefore, hindering the diffusion of water molecules inside it. The computational tool to perform the method discussed here is available on https://github.com/crobertocamilo/MD-permeation.

Nanocomputational Observation of Interaction of Two Cytotoxins and Nanobio Membrane: Molecular Dynamics Simulation Study

2011 ◽  
Vol 110-116 ◽  
pp. 3888-3892
Author(s):  
N. Maftouni ◽  
M. Amininassab ◽  
F. Kowsari
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Small Proteins ◽  
Steered Molecular Dynamics Simulation ◽  
The Difference ◽  
Dynamics Simulations ◽  
Naja Atra

Experimental observations have shown that cardio toxins (cobra cytotoxins), small proteins of three-fingered cytotoxin group, damage nanobiomembranes in different cells and vesicles. However, the molecular mechanism of this damage is not yet completely cleared. Molecular dynamics simulations have been used here to study the interaction of cardiotoxins A3 and A4 from Naja atra cobra venom with hydrated 1-palmitoyl-2-oleoyl-1-sn-3-phosphatidylcholine (POPC) lipid bilayer in two separate systems. Each of studied systems included one cytotoxin molecule, 128 lipid molecules (64 molecules in each monolayer) and 11817 water molecules. It has been found that the toxin interacts with zwitterionic bilayer formed by POPC. At the beginning of simulation the cytotoxins have been oriented toward nanobiomembrane surface by their loops’ tips. This orientation has changed during first 50 ns of classical molecular dynamics simulation for both of studied cytotoxins. The A3 toxin finally meets POPC nanobiomembrane with sides of loops near tips including cytotoxin region THR148 and VAL155. The A4 cytotoxin molecule has been finally oriented toward surface of nanobiomembrane with base and one of loop's tip including THR184, ARG186 and LEU158 amino acids, after 50 ns molecular dynamics simulation. Then 25 ns steered molecular dynamics simulation has been done for both of systems. The obtained data suggest that cytotoxin A3 meets the nanobiomembrane with sides of loops near tips and A4 meets POPC nanobiomembrane with base and one of loop's tips. The difference between final orientations of these two cytotoxins comes from the difference in the structure of them.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

scholarly journals Reactive molecular dynamics simulation of the high-temperature pyrolysis of 2,2′,2′′,4,4′,4′′,6,6′,6′′-nonanitro-1,1′:3′,1′′-terphenyl (NONA)

RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5507-5515
Author(s):  
Liang Song ◽  
Feng-Qi Zhao ◽  
Si-Yu Xu ◽  
Xue-Hai Ju
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Reactive Molecular Dynamics ◽  
Ring Compounds ◽  
Fused Ring ◽  
Dynamics Simulations

The bimolecular and fused ring compounds are found in the high-temperature pyrolysis of NONA using ReaxFF molecular dynamics simulations.

scholarly journals The Impact of the Electric Field on Surface Condensation of Water Vapor: Insight from Molecular Dynamics Simulation

Nanomaterials ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 64 ◽  
Author(s):  
Qin Wang ◽  
Hui Xie ◽  
Zhiming Hu ◽  
Chao Liu
Keyword(s):  
Molecular Dynamics ◽  
Water Vapor ◽  
Electric Field ◽  
Intermolecular Forces ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Attraction Force ◽  
Condensation Rate ◽  
Shape Transformation ◽  
The Impact

In this study, molecular dynamics simulations were carried out to study the coupling effect of electric field strength and surface wettability on the condensation process of water vapor. Our results show that an electric field can rotate water molecules upward and restrict condensation. Formed clusters are stretched to become columns above the threshold strength of the field, causing the condensation rate to drop quickly. The enhancement of surface attraction force boosts the rearrangement of water molecules adjacent to the surface and exaggerates the threshold value for shape transformation. In addition, the contact area between clusters and the surface increases with increasing amounts of surface attraction force, which raises the condensation efficiency. Thus, the condensation rate of water vapor on a surface under an electric field is determined by competition between intermolecular forces from the electric field and the surface.

scholarly journals Electrical Breakdown Mechanism of Transformer Oil with Water Impurity: Molecular Dynamics Simulations and First-Principles Calculations

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 123
Author(s):  
Bin Cao ◽  
Ji-Wei Dong ◽  
Ming-He Chi
Keyword(s):  
Molecular Dynamics ◽  
Thermal Diffusion ◽  
First Principles ◽  
Electrical Breakdown ◽  
Transformer Oil ◽  
Water Molecules ◽  
Conducting Channel ◽  
Breakdown Mechanism ◽  
Water Impurity ◽  
Dynamics Simulations

Water impurity is the essential factor of reducing the insulation performance of transformer oil, which directly determines the operating safety and life of a transformer. Molecular dynamics simulations and first-principles electronic-structure calculations are employed to study the diffusion behavior of water molecules and the electrical breakdown mechanism of transformer oil containing water impurities. The molecular dynamics of an oil-water micro-system model demonstrates that the increase of aging acid concentration will exponentially expedite thermal diffusion of water molecules. Density of states (DOS) for a local region model of transformer oil containing water molecules indicates that water molecules can introduce unoccupied localized electron-states with energy levels close to the conduction band minimum of transformer oil, which makes water molecules capable of capturing electrons and transforming them into water ions during thermal diffusion. Subsequently, under a high electric field, water ions collide and impact on oil molecules to break the molecular chain of transformer oil, engendering carbonized components that introduce a conduction electronic-band in the band-gap of oil molecules as a manifestation of forming a conductive region in transformer oil. The conduction channel composed of carbonized components will be eventually formed, connecting two electrodes, with the carbonized components developing rapidly under the impact of water ions, based on which a large number of electron carriers will be produced similar to “avalanche” discharge, leading to an electrical breakdown of transformer oil insulation. The water impurity in oil, as the key factor for forming the carbonized conducting channel, initiates the electric breakdown process of transformer oil, which is dominated by thermal diffusion of water molecules. The increase of aging acid concentration will significantly promote the thermal diffusion of water impurities and the formation of an initial conducting channel, accounting for the degradation in dielectric strength of insulating oil containing water impurities after long-term operation of the transformer.

scholarly journals Origin and control of ionic hydration patterns in nanopores

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Miraslau L. Barabash ◽  
William A. T. Gibby ◽  
Carlo Guardiani ◽  
Alex Smolyanitsky ◽  
Dmitry G. Luchinsky ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Water Molecules ◽  
Surrounding Water ◽  
Ionic Hydration ◽  
Hydration Shells ◽  
Water Layers ◽  
Dynamics Simulations ◽  
And Control

AbstractIn order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. Here, we study the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in a graphene nanopore in terms of experimentally accessible radial distribution functions, giving results that agree well with molecular dynamics simulations. The patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the graphene membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns.

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