A multi-scale molecular dynamics study of the assembly of micron-size supraparticles from 30 nm alkyl-coated nanoparticles

2013 ◽  
Vol 15 (21) ◽  
pp. 8132 ◽  
Author(s):  
Damien Thompson ◽  
Mateusz Sikora ◽  
Piotr Szymczak ◽  
Marek Cieplak
Keyword(s):  
Molecular Dynamics ◽  
Multi Scale ◽  
Coated Nanoparticles ◽  
Micron Size

Simulating Surface Forces Between Iron Oxide Surfaces Immersed in Methyl Oleate Using Molecular Dynamics

2018 ◽  
Author(s):  
William W. F. Chong ◽  
Hedong Zhang
Keyword(s):  
Molecular Dynamics ◽  
Iron Oxide ◽  
Methyl Oleate ◽  
Md Simulation ◽  
Surface Forces ◽  
Oxide Surfaces ◽  
Load Bearing ◽  
Multi Scale ◽  
Molecular Potentials ◽  
Solvation Forces

Using Molecular Dynamics (MD) simulation, the current study determined the surface forces between iron oxide surfaces when immersed in methyl oleate. Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) force field was used to model the methyl oleate molecules. For the nano-confinement simulation, the iron oxide wall was modelled from its crystal structure. The nano-confinement simulation model was setup in a manner where the confined methyl oleate molecules were in contact with the bulk molecules surrounding each side of the iron oxide walls. Through the simulation, the load-separation gap profile was obtained by reducing the separation gap between the ferric oxide walls. When the separation gap was reduced from 2.75 nm to 1.88 nm, the load is shown to increase monotonically. Such increase in load bearing ability of the contact is observed to correspond to a more densely packed methyl oleate molecules, reflected by four well-formed layers across the separation gap. As the gap is dropped from 1.88 nm to 1.63 nm, the load instead reduces, indicating deteriorating load bearing ability of the contact. However, the load bearing ability of the contact is then shown to recover when the gap was further reduced till 1.38 nm. This oscillatory load trend is shown to be as a result of a layer of methyl oleate molecules being squeezed out of contact, corroborated by the density profile change where four well-formed layers were reduced to only three layers from 1.88 nm to 1.38 nm gap. This also indicates that the simulated contact exhibits structural forces, known as solvation forces. Thus, the MD simulation discussed in this study is demonstrated to be capable of providing a foundation to allow for a multi-scale simulation, integrating various force laws at different length scales, to study larger scale tribological contacts.

A multi-scale molecular dynamics simulation of PMAL facilitated delivery of siRNA

RSC Advances ◽  
2015 ◽  
Vol 5 (83) ◽  
pp. 68227-68233 ◽  
Author(s):  
Jipeng Li ◽  
Yiyun Ouyang ◽  
Xian Kong ◽  
Jingying Zhu ◽  
Diannan Lu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Lipid Bilayer ◽  
Dynamics Simulation ◽  
Lipid Bilayer Membranes ◽  
Bilayer Membranes ◽  
Multi Scale

PMAL as a novel carrier for the delivery of siRNA into lipid bilayer membranes.

scholarly journals Multi-Scale Modeling of Aqueous-Phase Methane Diffusion in Silicate Channels

2021 ◽  
Author(s):  
Tom Pace ◽  
Hadi Rahmaninejad ◽  
Bin Sun ◽  
Peter Kekenes-Huskey
Keyword(s):  
Molecular Dynamics ◽  
Multi Scale ◽  
Relative Contribution ◽  
Kinetic Information ◽  
Two Factors ◽  
Molecule Transport ◽  
Potentials Of Mean Force ◽  
Methane Diffusion ◽  
Dynamics Simulations ◽  
Small Molecule Transport

Silica-based materials including zeolites are commonly used for wide ranging applications including separations and catalysis.<br>Substrate transport rates in these materials often significantly influence the efficiency of such applications.<br>Two factors that contribute to transport rates include<br>1) the porosity of the silicate matrix and<br>2) non-bonding interactions between the diffusing species and the silicate surface.<br>Here, we utilize computer simulation to resolve the relative contribution of these factors to effective methane transport rates in a silicate channel.<br>Specifically, we develop a `homogenized' model of methane transport valid at micron and longer length scales that incorporates atomistic-scale kinetic information.<br>The atomistic-scale data are obtained from extensive molecular dynamics simulations that yield local diffusion coefficients and potentials of mean force.<br>With this model, we demonstrate how nuances in silicate hydration and silica/methane interactions impact 'macroscale' methane diffusion rates in bulk silicate materials.<br>This hybrid homogenization/molecular dynamics approach will be of general use for describing small molecule transport in materials with detailed molecular interactions.<br><br>

MOLECULAR ELEMENT METHOD (MEM) FOR MULTI-SCALE MODELING AND SIMULATIONS OF NANO/MICRO-SYSTEMS

2005 ◽  
Vol 29 (3) ◽  
pp. 403-421
Author(s):  
Kamran Behdinan ◽  
Yigui Xu ◽  
Zouheir Fawaz
Keyword(s):  
Molecular Dynamics ◽  
Classical Method ◽  
Computational Time ◽  
Physical Parameters ◽  
Modeling And Simulations ◽  
Multi Scale ◽  
Scale Modeling ◽  
Multi Scale Modeling ◽  
Micro Systems ◽  
Element Method

A new technique called Molecular Element Method is proposed for multi-scale modeling and simulations of nano/micro-systems. In this technique, the system is divided into molecular elements whose properties are represented by sets of equivalent physical parameters obtained from atomic information. The discrete system is solved based on continuum mechanics theories. The resultant element information from system solving is then used as an external constraint for the elements, to investigate the atomic information within, using molecular dynamics calculations. Both system properties and atomic information at local zones can be obtained accurately and efficiently in this way, A crystal of Cu having 285,883 atoms with a through the thickness hole inside is investigated using this technique. Tension stresses of the crystal and the slip of atoms around the hole’s edge are revealed corresponding to five strain loads. Compared with the results obtained from the classical molecular dynamics method, the maximum stress error is 2.7%, while the computational time is only 7.2-11.8% of that taken by the classical method.

scholarly journals Multi-scale approach for modeling stability, aggregation, and network formation of nanoparticles suspended in aqueous solutions

Nanoscale ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 3979-3992 ◽  
Author(s):  
Annalisa Cardellini ◽  
Matteo Alberghini ◽  
Ananth Govind Rajan ◽  
Rahul Prasanna Misra ◽  
Daniel Blankschtein ◽  
...  
Keyword(s):  
Aqueous Solutions ◽  
Network Formation ◽  
Computational Framework ◽  
Multi Scale ◽  
Coated Nanoparticles

Multi-scale computational framework to investigate interactions between bare and surfactant-coated nanoparticles in aqueous solutions beyond classical DLVO and aggregation theories.

A MULTI-SCALE NONEQUILIBRIUM MOLECULAR DYNAMICS ALGORITHM AND ITS APPLICATIONS

2009 ◽  
Vol 01 (03) ◽  
pp. 405-420 ◽  
Author(s):  
NI SHENG ◽  
SHAOFAN LI
Keyword(s):  
Molecular Dynamics ◽  
Local Equilibrium ◽  
Random Force ◽  
Coarse Grained ◽  
Nonequilibrium Molecular Dynamics ◽  
Fine Scale ◽  
Coarse Scale ◽  
Fe Method ◽  
Time Step ◽  
Multi Scale

In this paper, we introduce a multi-scale nonequilibrium molecular dynamics (MS-NEMD) model that is capable of simulating nano-scale thermal–mechanical interactions. Recent simulation results using the MS-NEMD model are presented. The MS-NEMD simulation generalises the nonequilibrium molecular dynamics (NEMD) simulation to the setting of concurrent multi-scale simulation. This multi-scale framework is based on a novel concept of multi-scale canonical ensemble. Under this concept, each coarse scale finite element (FE) node acts as a thermostat, while the atoms associated with each node are assumed to be in a local equilibrium state within one coarse scale time step. The coarse scale mean field is solved by the FE method based on a coarse-grained thermodynamics model; whereas in the fine scale the NEMD simulation is driven by the random force that is regulated by the inhomogeneous continuum filed through a distributed Nośe–Hoover thermostat network. It is shown that the fine scale distribution function is canonical in the sense that it obeys a drifted local Boltzmann distribution.

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