scholarly journals Subatomic-Level Solid/Fluid Boundary of Lennard-Jones Atoms: A Molecular Dynamics Study of Metal-Inert Fluid Interface

2019 ◽  
Vol 9 (12) ◽  
pp. 2439 ◽  
Author(s):  
Yechan Noh ◽  
Truong Vo ◽  
BoHung Kim
Keyword(s):  
Molecular Dynamics ◽  
Thermodynamic Properties ◽  
Slip Length ◽  
Mathematical Expression ◽  
Md Simulations ◽  
Kapitza Resistance ◽  
Fluid Interface ◽  
Lennard Jones ◽  
Fluid Boundary ◽  
Definition Of

At the molecular scale, the definition of solid/fluid boundary is ambiguous since its defining precision is comparable to the size of the electron orbitals. It is important to figure out the sub-atomic-level solid/fluid boundary as the definition of the solid/fluid interface is related to estimating various properties such as slip length, Kapitza resistance, confined volume, thermodynamic properties, and material properties. In this work, molecular dynamics (MD) simulations were conducted to show the effects of the solid/fluid boundary on estimating thermodynamic properties. Our results reveal that the different definitions of solid/fluid boundary can cause a considerable impact on quantitative analysis and even qualitative analysis of a nanoscale system. The solid/fluid boundary for Lennard-Jones atoms is determined within sub-atomic precision via heat transfer MD simulations and microscopic heat flux relation. The result shows that solid/fluid boundary is slightly shifted to the fluid regime as the temperature increase. We suggested a mathematical expression of solid/fluid boundary of LJ atom that is theoretically estimated by ignoring the thermal vibration. The results presented in this work are expected to improve the accuracy of analyzing nanoscale phenomena as well as the continuum-based models for nanoscale heat and mass transport.

Surface Tension Evaluation Via Thermodynamic Analysis of Statistical Data From Molecular Dynamics Simulations

Volume 4 ◽  
2004 ◽  
Author(s):  
Aaron P. Wemhoff ◽  
Van P. Carey
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Density Profile ◽  
Md Simulation ◽  
Md Simulations ◽  
Bulk Liquid ◽  
Interfacial Region ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Lennard Jones

Surface tension determination of liquid-vapor interfaces of polyatomic fluids using traditional methods has shown to be difficult due to the requirement of evaluating complex intermolecular potentials. However, analytical techniques have recently been developed that determine surface tension solely by means of the characteristics of the interfacial region between the bulk liquid and vapor regions. A post-simulation application of the excess free energy density integration (EFEDI) method was used for analysis of the resultant density profile of molecular dynamics (MD) simulations of argon using a simple Lennard-Jones potential and diatomic nitrogen using a two-center Lennard-Jones potential. MD simulations were also run for an approximation of nitrogen using the simple Lennard-Jones potential. In each MD simulation, a liquid film was initialized between vapor regions and NVE-type simulations were run to equilibrium. The simulation domain was divided into bins across the interfacial region for fluid density collection, and the resultant interfacial region density profile was used for surface tension evaluation. Application of the EFEDI method to these MD simulation results exhibited good approximations to surface tension as a function of temperature for both a simple and complex potential.

MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics

2019 ◽  
Author(s):  
David De Sancho ◽  
Anne Aguirre
Keyword(s):  
Molecular Dynamics ◽  
Master Equation ◽  
Md Simulations ◽  
Distinctive Features ◽  
Markov State Models ◽  
Software Packages ◽  
Long Time ◽  
State Models ◽  
Definition Of ◽  
Kinetics Of

<div>Markov state models (MSMs) have become one of the most important techniques for understanding biomolecular transitions from classical molecular dynamics (MD) simulations. MSMs provide a systematized way of accessing the long time kinetics of the system of interest from the short-timescale microscopic transitions observed in simulation trajectories. At the same time, they provide a consistent description of the equilibrium and dynamical properties of the system of interest, and they are ideally suited for comparisons against experiment. A few software packages exist for building MSMs, which have been widely adopted. Here we introduce MasterMSM, a new Python package that uses the master equation formulation of MSMs and provides a number of new algorithms for building and analyzing these models. We demonstrate some of the most distinctive features of the package, including the estimation of rates, definition of core-sets for transition based assignment of states, the estimation of committors and fluxes, and the sensitivity analysis of the emerging networks. The package is available at https://github.com/daviddesancho/MasterMSM.</div>

Hydrogen Adsorption of Carbon Nanocone Arrays: Influences of Cone Arrangements

2013 ◽  
Vol 845 ◽  
pp. 345-349
Author(s):  
I Ling Chang ◽  
Ming Liang Liao ◽  
Chi Hsiang Chuang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Adsorption ◽  
Md Simulations ◽  
Critical Value ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Weight Percentage ◽  
Curvature Effects ◽  
Lennard Jones ◽  
Potential Parameters

This paper used molecular dynamics (MD) simulations to investigate influences of cone arrangements (including the cone orientation, arrangement pattern and cone spacing) on hydrogen adsorption of open-tip carbon nanocone (CNC) arrays at temperatures of 100 and 300 K. To consider curvature effects for the cone structure of the CNCs, the curvature-modified Lennard-Jones potential parameters were adopted to describe the interactions between the hydrogen and carbon atoms. It was found that the cone orientation (aligned, opposite, and alternate) does not have obvious influences on hydrogen adsorption of the CNC arrays. The arrangement pattern (square and triangular), however, had significant influences on the hydrogen adsorption. The square-patterned CNC array was noticed to have higher storage weight percentage than the triangular-patterned one. Regarding to the influences of cone spacing, the storage weight percentage grew with the increase of the cone spacing and arrived at a stable value as the cone spacing reached a certain critical value. The influences cone arrangements could be ascribed to repulsive effects, which are evident as cone spacing become narrow.

A MOLECULAR DYNAMICS SIMULATION STUDY OF THE POLYHEDRAL STRUCTURE OF LIQUID ARGON DURING GLASS TRANSITION

2009 ◽  
Vol 23 (08) ◽  
pp. 1069-1075
Author(s):  
CONG LI ◽  
DAN WANG ◽  
JIAYUN LI ◽  
YONGPING DUAN ◽  
MEILI LI ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Glass Transition ◽  
Solidification Process ◽  
Md Simulations ◽  
Liquid Argon ◽  
Dynamics Simulation ◽  
Angle Distribution ◽  
Lennard Jones ◽  
Bond Angle Distribution ◽  
Order Increase

Polyhedron structures changes in Lennard–Jones (LJ) liquid argon containing 108 atoms are investigated by means of molecular dynamics (MD) simulations during the glass transition. The local bond orientational parameter and the bond angle distribution are calculated. In particular, a new parameter is introduced to simultaneously quantify the changes of all the major polyhedral structures: tetrahedron, hexahedron, octahedron, dodecahedron, and icosahedron. The results show that icosahedral order, hexahedral order and octahedral order increase with decreasing temperature, while tetrahedral order and dodecahedral order decrease. This indicates that the glass transition is a solidification process with complex microstructure changes.

Molecular Dynamics Simulations of Thermal Interactions in Nanoscale Liquid Channels

2008 ◽  
Author(s):  
BoHung Kim ◽  
Ali Beskok ◽  
Tahir Cagin
Keyword(s):  
Molecular Dynamics ◽  
Thermal Resistance ◽  
Md Simulations ◽  
Kapitza Resistance ◽  
Fourier Law ◽  
Thermal Exchange ◽  
Nano Scale ◽  
Thermal Oscillation ◽  
Temperature Jumps ◽  
Dynamics Simulations

Molecular Dynamics (MD) simulations of nano-scale flows typically utilize fixed lattice crystal interactions between the fluid and stationary wall molecules. This approach cannot properly model thermal exchange at the wall-fluid interface. Therefore, we use an interactive thermal wall model that can properly simulate the flow and heat transfer in nano-scale channels. Using the interactive thermal wall, Fourier law of heat conduction is verified for the 3.24 nm channel, while the thermal conductivity obtained from Fourier law is verified using the predictions of Green-Kubo theory. Moreover, temperature jumps at the liquid/solid interface, corresponding to the well known Kapitza resistance, are observed. Using systematic studies thermal resistance length at the interface is characterized as a function of the surface wettability, thermal oscillation frequency, wall temperature and thermal gradient. An empirical model for the thermal resistance length, which could be used as the jump-coefficient of a Navier boundary condition, is developed.

MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics

2019 ◽  
Author(s):  
David De Sancho ◽  
Anne Aguirre
Keyword(s):  
Molecular Dynamics ◽  
Master Equation ◽  
Md Simulations ◽  
Distinctive Features ◽  
Markov State Models ◽  
Software Packages ◽  
Long Time ◽  
State Models ◽  
Definition Of ◽  
Kinetics Of

<div>Markov state models (MSMs) have become one of the most important techniques for understanding biomolecular transitions from classical molecular dynamics (MD) simulations. MSMs provide a systematized way of accessing the long time kinetics of the system of interest from the short-timescale microscopic transitions observed in simulation trajectories. At the same time, they provide a consistent description of the equilibrium and dynamical properties of the system of interest, and they are ideally suited for comparisons against experiment. A few software packages exist for building MSMs, which have been widely adopted. Here we introduce MasterMSM, a new Python package that uses the master equation formulation of MSMs and provides a number of new algorithms for building and analyzing these models. We demonstrate some of the most distinctive features of the package, including the estimation of rates, definition of core-sets for transition based assignment of states, the estimation of committors and fluxes, and the sensitivity analysis of the emerging networks. The package is available at https://github.com/daviddesancho/MasterMSM.</div>

Molecular Dynamics Simulations of Fluid Flow in a Rotating Channel

2005 ◽  
Author(s):  
Zhaohui Qin
Keyword(s):  
Molecular Dynamics ◽  
Fluid Flow ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Lennard Jones ◽  
Nano Scale ◽  
Dynamics Simulations ◽  
Rotating Channel

Molecular dynamics (MD) simulations of a Lennard-Jones liquid flowing through a rotating nano-scale channel are presented.

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