Microhydrodynamics with Dissipative Particle Dynamics

1995 ◽  
Vol 407 ◽  
Author(s):  
Pep Español ◽  
Ignacio Zúñiga
Keyword(s):  
Simple Model ◽  
Molecular Dynamic Simulation ◽  
Dynamic Simulation ◽  
Theoretical Foundation ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Model Parameters ◽  
Hydrodynamic Properties ◽  
Insight Into

ABSTRACTDissipative particle dynamics is essentially a coarse-grained molecular dynamic simulation technique that captures the essential physics with considerably less computer effort. We have given a sound theoretical foundation to the technique with respect to the equilibrium and hydrodynamic properties. In this paper we further explore the connection of the model parameters of DPD with the underlying microscopic dynamics for the case of a simple model of a solid. This provides some insight into the difficulties of interpretation of DPD simulations.

Systematic design and application of unimolecular star-like block copolymer micelles: a coarse-grained simulation study

2016 ◽  
Vol 18 (38) ◽  
pp. 26519-26529 ◽  
Author(s):  
Xiaofang Zhang ◽  
Wenjing Lin ◽  
Liyang Wen ◽  
Na Yao ◽  
Shuyu Nie ◽  
...  
Keyword(s):  
Block Copolymer ◽  
Polymeric Micelles ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Systematic Design ◽  
Block Copolymer Micelles ◽  
Copolymer Micelles ◽  
Dynamics Simulations ◽  
Insight Into

We provide a mesoscopic insight into the micellar behavior of unimolecular polymeric micelles via dissipative particle dynamics simulations.

THE SIMULATION OF POLYSTYRENE/NANOPARTICLES COMPOSITE MICROSPHERES USING DISSIPATIVE PARTICLE DYNAMICS

2013 ◽  
Vol 12 (02) ◽  
pp. 1250111 ◽  
Author(s):  
HAILONG XU ◽  
QIUYU ZHANG ◽  
HEPENG ZHANG ◽  
BAOLIANG ZHANG ◽  
CHANGJIE YIN
Keyword(s):  
Dissipative Particle Dynamics ◽  
Sodium Dodecyl ◽  
Coarse Graining ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Polystyrene Nanoparticles ◽  
Coarse Grained Model ◽  
Composite Microspheres ◽  
Polystyrene Matrix ◽  
Materials Studio

Dissipative particle dynamics (DPD) was initially used to simulate the polystyrene/nanoparticle composite microspheres (PNCM) in this paper. The coarse graining model of PNCM was established. And the DPD parameterization of the model was represented in detail. The DPD repulsion parameters were calculated from the cohesive energy density which could be calculated by amorphous modules in Materials Studio. The equilibrium configuration of the simulated PNCM shows that the nanoparticles were actually "modified" with oleic acid and the modified nanoparticles were embedded in the bulk of polystyrene. As sodium dodecyl sulfate (SDS) was located in the interface between water and polystyrene, the hydrophilic head of SDS stretched into water while the hydrophobic tailed into polystyrene. All simulated phenomena were consistent with the experimental results in preparation of polystyrene/nanoparticles composite microspheres. The effect of surface modification of nanoparticles on its dispersion in polystyrene matrix was also studied by adjusting the interaction parameters between the OA and NP beads. The final results indicated that the nanoparticles removed from the core of composite microsphere to the surface with increase of a OA-NP . All the simulated results demonstrated that our coarse–grained model was reasonable.

scholarly journals A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

Soft Matter ◽  
2021 ◽  
Author(s):  
Rakesh K Vaiwala ◽  
Ganapathy Ayappa
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dissipative Particle Dynamics ◽  
Protein Structures ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Native Protein ◽  
Dynamics Simulations

A coarse-grained force field for molecular dynamics simulations of native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by...

Understanding receptor-mediated endocytosis of elastic nanoparticles through coarse grained molecular dynamic simulation

2018 ◽  
Vol 20 (24) ◽  
pp. 16372-16385 ◽  
Author(s):  
Zhiqiang Shen ◽  
Huilin Ye ◽  
Ying Li
Keyword(s):  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Contact Area ◽  
Late Stage ◽  
Early Stage ◽  
Coarse Grained ◽  
Large Energy ◽  
Receptor Mediated Endocytosis ◽  
Large Contact Area

The membrane wrapping of the soft nanoparticle (NP) is faster than that of the stiff one at the early stage, due to the NP deformation induced large contact area between the NP and membrane. However, because of the large energy penalties induced by the NP deformation, the membrane wrapping speed of soft NPs slows down during the late stage.

SIMULATION OF THE ALCOHOL-OIL MIXTURE IN A T-SHAPED MICROCHANNEL USING THE DISSIPATIVE PARTICLE DYNAMICS METHOD ON GPU DEVICES

2014 ◽  
Vol 13 (1) ◽  
pp. 65
Author(s):  
A. A. Horta ◽  
L. O. S. Ferreira ◽  
E. L. Martinez ◽  
R. Maciel Filho
Keyword(s):  
Dissipative Particle Dynamics ◽  
Fluid Motion ◽  
Particle Dynamics ◽  
Immiscible Fluids ◽  
Biodiesel Production ◽  
Model Parameters ◽  
Processing Unit ◽  
Fluid Properties ◽  
Practical Engineering ◽  
Multiphase Fluid

Multiphase fluid motion in microchannnels involves complicated fluid dynamics and is fundamentally important to diverse practical engineering applications. Among several applications, the alcohol-oil mixture is particularly important due to its application for biodiesel production. In this work, the mixture of immiscible fluids alcohol-oil in a square T-shaped microchannel was investigated using the Dissipative Particle Dynamics (DPD) method available in the HOOMD simulator, which runs on a single graphic processing unit (GPU). The immiscible fluids were achieved by increasing the repulsive force between species. The fluid properties and hydrodynamic behavior were discussed in function of model parameters. The simulation results agree with data published in the literature showing that the DPD is appropriate for simulation of mass transport on complex geometries in microscale on a single GPU.

Computer Simulation of Vesicle Fusion

2011 ◽  
Vol 474-476 ◽  
pp. 943-948
Author(s):  
Shao Gui Wu ◽  
Hong Xia Guo
Keyword(s):  
Computer Simulation ◽  
Molecular Level ◽  
Dissipative Particle Dynamics ◽  
Simulation Method ◽  
Particle Dynamics ◽  
Vesicle Fusion ◽  
Simulation System ◽  
Dynamics Simulation ◽  
Dissipative Particle Dynamics Simulation ◽  
Insight Into

A dissipative particle dynamics simulation method is used to get insight into molecular-level details of vesicle fusion in this study. For simplicity, the simulation system contains water and amphiphiles. The fusion mechanism is investigated in detail. It is found that the whole fusion process is in well agreement with the “stalk-pore” hypothesis. The dynamics of vesicle fusion is analyzed by monitoring the time evolutions of morphologies.

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