A comparative study between dissipative particle dynamics and molecular dynamics for simple- and complex-geometry flows

2005 ◽  
Vol 123 (10) ◽  
pp. 104107 ◽  
Author(s):  
Eric E. Keaveny ◽  
Igor V. Pivkin ◽  
Martin Maxey ◽  
George Em Karniadakis
Keyword(s):  
Molecular Dynamics ◽  
Comparative Study ◽  
Complex Geometry ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics

Multiscale Modeling of Flow Induced Thrombogenicity Using Dissipative Particle Dynamics and Molecular Dynamics

2013 ◽  
Author(s):  
Danny Bluestein ◽  
João S. Soares ◽  
Peng Zhang ◽  
Chao Gao ◽  
Seetha Pothapragada ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Blood Flow ◽  
Red Blood Cells ◽  
Platelet Activation ◽  
Blood Cells ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Coagulation Cascade ◽  
Shear Stresses ◽  
Activated Platelets

The coagulation cascade of blood may be initiated by flow induced platelet activation, which prompts clot formation in prosthetic cardiovascular devices and arterial disease processes. While platelet activation may be induced by biochemical agonists, shear stresses arising from pathological flow patterns enhance the propensity of platelets to activate and initiate the intrinsic pathway of coagulation, leading to thrombosis. Upon activation platelets undergo complex biochemical and morphological changes: organelles are centralized, membrane glycoproteins undergo conformational changes, and adhesive pseudopods are extended. Activated platelets polymerize fibrinogen into a fibrin network that enmeshes red blood cells. Activated platelets also cross-talk and aggregate to form thrombi. Current numerical simulations to model this complex process mostly treat blood as a continuum and solve the Navier-Stokes equations governing blood flow, coupled with diffusion-convection-reaction equations. It requires various complex constitutive relations or simplifying assumptions, and is limited to μm level scales. However, molecular mechanisms governing platelet shape change upon activation and their effect on rheological properties can be in the nm level scales. To address this challenge, a multiscale approach which departs from continuum approaches, may offer an effective means to bridge the gap between macroscopic flow and cellular scales. Molecular dynamics (MD) and dissipative particle dynamics (DPD) methods have been employed in recent years to simulate complex processes at the molecular scales, and various viscous fluids at low-to-high Reynolds numbers at mesoscopic scales. Such particle methods possess important properties at the mesoscopic scale: complex fluids with heterogeneous particles can be modeled, allowing the simulation of processes which are otherwise very difficult to solve by continuum approaches. It is becoming a powerful tool for simulating complex blood flow, red blood cells interactions, and platelet-mediated thrombosis involving platelet activation, aggregation, and adhesion.

scholarly journals Correction: Dissipative particle dynamics and molecular dynamics simulations on mesoscale structure and proton conduction in a SPEEK/PVDF-g-PSSA membrane

RSC Advances ◽  
2017 ◽  
Vol 7 (66) ◽  
pp. 41787-41787
Author(s):  
Yue Ma ◽  
Yuxiang Wang ◽  
Xuejian Deng ◽  
Guanggang Zhou ◽  
Shah Khalid ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Proton Conduction ◽  
Mesoscale Structure ◽  
Dynamics Simulations

Correction for ‘Dissipative particle dynamics and molecular dynamics simulations on mesoscale structure and proton conduction in a SPEEK/PVDF-g-PSSA membrane’ by Yue Ma et al., RSC Adv., 2017, 7, 39676–39684.

scholarly journals Dissipative particle dynamics and molecular dynamics simulations on mesoscale structure and proton conduction in a SPEEK/PVDF-g-PSSA membrane

RSC Advances ◽  
2017 ◽  
Vol 7 (63) ◽  
pp. 39676-39684 ◽  
Author(s):  
Yue Ma ◽  
Yuxiang Wang ◽  
Xuejian Deng ◽  
Guanggang Zhou ◽  
Sha Khalid ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Proton Conduction ◽  
Small Particles ◽  
Cluster Network ◽  
Mesoscale Structure ◽  
Dynamics Simulations

The blend morphologies evolve from disordered small particles to a regular PVDF cluster network, which were connected by SPEEK cylindrical channels.

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...

Temperature-Responsive Morphology Formation of PS-b-PI copolymer: A Dissipative Particle Dynamics Simulation Study

Soft Matter ◽  
2021 ◽  
Author(s):  
Natthiti Chiangraeng ◽  
Ukrit Keyen ◽  
Norio Yoshida ◽  
Piyarat Nimmanpipug
Keyword(s):  
Molecular Dynamics ◽  
Simulation Study ◽  
Diblock Copolymer ◽  
Self Assembly ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
Dynamics Simulation ◽  
Temperature Responsive ◽  
Classical Molecular Dynamics ◽  
Dissipative Particle Dynamics Simulation

Self-assembly responsiveness to stimuli of polystyrene-block-polyisoprene (PS-b-PI) diblock copolymer materials are explored by means of classical molecular dynamics (MD) and dissipative particle dynamics (DPD) simulations. A concerted relationship between the...

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