Molecular Dynamics Simulation of Evaporation of a Thin Liquid Argon Layer in a Closed System

2003 ◽  
Author(s):  
Y. W. Wu ◽  
Chin Pan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Liquid Film ◽  
Closed System ◽  
Thin Liquid Film ◽  
Liquid Argon ◽  
Dynamics Simulation ◽  
Jones Potential ◽  
Evaporation And Condensation ◽  
Simulation Based

Evaporation of a thin liquid film is of significant fundamental importance for both science and engineering applications. This work investigates the evaporation of a thin liquid argon layer into vacuum employing molecular dynamics simulation based on the Lennard-Jones potential. The simulation results demonstrate that the net evaporation rate of an ultra-thin liquid film into vacuum in a closed system may be modeled by the balance of evaporation and condensation based on the Schrage model. The evaporation/condensation coefficient and the non-Maxwellian factor may thus be evaluated. However, the coefficient thus obtained is sensitive to the dimension in the direction normal to the surface. It is also found that the mean temperature for the interface region is 2–3 K lower, while the temperature fluctuations are more violent, than that inside the liquid.

Nanostructures Length Effect on Phase Transition Phenomena of Ultra-Thin Liquid Film From a Nanostructured Surface: A Molecular Dynamics Study

2011 ◽  
Author(s):  
A. K. M. M. Morshed ◽  
T. C. Paul ◽  
Jamil A. Khan
Keyword(s):  
Molecular Dynamics ◽  
Film Thickness ◽  
Liquid Film ◽  
Solid Surface ◽  
Thin Liquid Film ◽  
Liquid Argon ◽  
Liquid Film Thickness ◽  
Dynamics Simulation ◽  
Phase System ◽  
Three Phase

A molecular dynamics simulation has been employed to investigate the boiling phenomena of few molecular-layer thin liquid-film adsorbed on a nanoscale roughened solid surface. The molecular system comprises of three phase system: solid platinum wall, liquid argon and argon vapor. A few layer of liquid argon has been placed on the nanoposts decorated solid surface where nanoposts ensemble surface roughness. Nanoposts height has been varied keeping liquid film thickness constant to capture three scenario: (i) Liquid-film thickness is higher than the height of the nanoposts (ii) Liquid-film and nanoposts are of same height (iii) Liquid-film thickness is less than the height of the nanoposts. Rest of the simulation box space has been filled with argon vapor. The simulation starts from the equilibrium three phase system and then suddenly the wall is heated to a higher temperature which resembles an ultra fast laser heating. Two different jump temperatures has been selected: one is a few degrees above the boiling point to initiate normal evaporation and the other one is far above the critical point temperature to initiate explosive boiling. Simulation results indicate nanostructures play significant role in both the cases. Argon responds very quickly in the nanoposts decorated surface and evaporation rate increases with the nanoposts height. Different boiling behavior has been observed for the nanoposts decorated surface.

Improved Sampling Strategies for Protein Model Refinement based on Molecular Dynamics Simulation

2020 ◽  
Author(s):  
Lim Heo ◽  
Collin Arbour ◽  
Michael Feig
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structure Prediction ◽  
Protein Structures ◽  
Conformational Space ◽  
Dynamics Simulation ◽  
Model Refinement ◽  
Protein Model ◽  
Lower Accuracy ◽  
Simulation Based

Protein structures provide valuable information for understanding biological processes. Protein structures can be determined by experimental methods such as X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, or cryogenic electron microscopy. As an alternative, in silico methods can be used to predict protein structures. Those methods utilize protein structure databases for structure prediction via template-based modeling or for training machine-learning models to generate predictions. Structure prediction for proteins distant from proteins with known structures often results in lower accuracy with respect to the true physiological structures. Physics-based protein model refinement methods can be applied to improve model accuracy in the predicted models. Refinement methods rely on conformational sampling around the predicted structures, and if structures closer to the native states are sampled, improvements in the model quality become possible. Molecular dynamics simulations have been especially successful for improving model qualities but although consistent refinement can be achieved, the improvements in model qualities are still moderate. To extend the refinement performance of a simulation-based protocol, we explored new schemes that focus on an optimized use of biasing functions and the application of increased simulation temperatures. In addition, we tested the use of alternative initial models so that the simulations can explore conformational space more broadly. Based on the insight of this analysis we are proposing a new refinement protocol that significantly outperformed previous state-of-the-art molecular dynamics simulation-based protocols in the benchmark tests described here. <br>

scholarly journals Investigation of the effect of Hydroxychloroquine, Remdesivir, Oseltamivir and some home remedies in the light of Molecular Dynamics Simulation

2020 ◽  
Author(s):  
Keka Talukdar
Keyword(s):  
Molecular Dynamics ◽  
Clinical Trial ◽  
Computer Simulation ◽  
Molecular Dynamics Simulation ◽  
Human Cell ◽  
Physical Modeling ◽  
Chemical Species ◽  
Dynamics Simulation ◽  
Spike Protein ◽  
Simulation Based

Modeling and simulation is another way of finding the interaction between different drugs and chemical species with human cell. Preliminary studies before clinical trial involve computer simulation based on the physical modeling so that clinical trial can be made easier. In many aspects of drug developing, simulation is an essential tool. Here molecular dynamics simulation is performed for the interaction of the spike protein of Covid-19 virus and some of the recently used drugs. Also, the effect of caffeine, theanine, nicotine etc on the virus is found by simulation

Thermal Conductivity Computation of Nanofluids by Equilibrium Molecular Dynamics Simulation: Nanoparticle Loading and Temperature Effect

2007 ◽  
Vol 1022 ◽  
Author(s):  
Suranjan Sarkar ◽  
R. Panneer Selvam
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Effective Thermal Conductivity ◽  
Copper Nanoparticles ◽  
Base Fluid ◽  
Liquid Argon ◽  
Dynamics Simulation ◽  
System Temperature ◽  
Solid Copper

AbstractA model nanofluid system of copper nanoparticles in argon base fluid was successfully modeled by molecular dynamics simulation. The interatomic interactions between solid copper nanoparticles, base liquid argon atoms and between solid copper and liquid argon were modeled by Lennard Jones potential with appropriate parameters. The effective thermal conductivity of the nanofluids was calculated through Green Kubo method in equilibrium molecular dynamics simulation for varying nanoparticle concentrations and for varying system temperatures. Thermal conductivity of the basefluid was also calculated for comparison. This study showed that effective thermal conductivity of nanofluids is much higher than that of the base fluid and found to increase with increased nanoparticle concentration and system temperature. Through molecular dynamics calculation of mean square displacements for basefluid, nanofluid and its components, we suggested that the increased movement of liquid atoms in the presence of nanoparticle was probable mechanism for higher thermal conductivity of nanofluids.

Molecular Dynamics Study on Explosive Boiling of Thin Liquid Argon Film on Nanostructured Surface Under Different Wetting Conditions

2015 ◽  
Author(s):  
Sheikh Mohammad Shavik ◽  
Mohammad Nasim Hasan ◽  
A. K. M. Monjur Morshed
Keyword(s):  
Molecular Dynamics ◽  
Liquid Film ◽  
Solid Surface ◽  
Solid Wall ◽  
Thin Liquid Film ◽  
Liquid Argon ◽  
Spatial And Temporal Variation ◽  
Phase System ◽  
Explosive Boiling ◽  
System Pressure

Molecular dynamics (MD) simulations have been performed to investigate the boiling phenomena of thin liquid film adsorbed on a nanostructured solid surface with particular emphasis on the effect of wetting condition of the solid surface. The molecular system consists of liquid and vapor argon, and solid platinum wall. The nanostructures which reside on top of the solid wall have shape of rectangular block. The solid-liquid interfacial wettability, in other words whether the solid surface is hydrophilic or hydrophobic has been altered for different cases to examine its effect on boiling phenomena. The initial configuration of the simulation domain comprised a three phase system (solid platinum, liquid argon and vapor argon) which was equilibrated at 90 K. After equilibrium period, the wall temperature was suddenly increased from 90 K to 250 K which is far above the critical point of argon and this initiates rapid or explosive boiling. The spatial and temporal variation of temperature and density as well as the variation of system pressure with respect to time were closely monitored for each case. The heat flux normal to the solid surface was also calculated to illustrate the effectiveness of heat transfer for different cases of wetting conditions of solid surface. The results show that the wetting condition of surface has significant effect on explosive boiling of the thin liquid film. The surface with higher wettability (hydrophilic) provides more favorable conditions for boiling than the low-wetting surface (hydrophobic) and therefore, liquid argon responds quickly and shifts from liquid to vapor phase faster in case of hydrophilic surface.

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