Coarse-grained Particle Method Research Articles

Investigation of red blood cell mechanical properties using AFM indentation and coarse-grained particle method

BackgroundRed blood cells (RBCs) deform significantly and repeatedly when passing through narrow capillaries and delivering dioxygen throughout the body. Deformability of RBCs is a key characteristic, largely governed by the mechanical properties of the cell membrane. This study investigated RBC mechanical properties using atomic force microscopy (AFM) with the aim to develop a coarse-grained particle method model to study for the first time RBC indentation in both 2D and 3D. This new model has the potential to be applied to further investigate the local deformability of RBCs, with accurate control over adhesion, probe geometry and position of applied force.ResultsThe model considers the linear stretch capacity of the cytoskeleton, bending resistance and areal incompressibility of the bilayer, and volumetric incompressibility of the internal fluid. The model’s performance was validated against force–deformation experiments performed on RBCs under spherical AFM indentation. The model was then used to investigate the mechanisms which absorbed energy through the indentation stroke, and the impact of varying stiffness coefficients on the measured deformability. This study found the membrane’s bending stiffness was most influential in controlling RBC physical behaviour for indentations of up to 200 nm.ConclusionsAs the bilayer provides bending resistance, this infers that structural changes within the bilayer are responsible for the deformability changes experienced by deteriorating RBCs. The numerical model presented here established a foundation for future investigations into changes within the membrane that cause differences in stiffness between healthy and deteriorating RBCs, which have already been measured experimentally with AFM.

Assessment of Different Discrete Particle Methods Ability To Predict Gas-Particle Flow in a Small-Scale Fluidized Bed

Several discrete particle methods exist in the open literature to simulate fluidized bed systems, such as discrete element method (DEM), time-driven hard sphere (TDHS), coarse-grained particle method (CGPM), coarse grained hard sphere (CGHS), and multiphase particle-in-cell (MP-PIC). The main difference between these methods is in the treatment of particle–particle interactions: by calculating collision forces (DEM and CGPM), using momentum conservation laws (TDHS and CGHS), or based on the particle stress model (MP-PIC). Here, these methods are compared by simulating the same small-scale fluidized bed with the same open-source code MFIX. The results indicate that both modeling the particle–particle collision by TDHS and lumping a few particles in a parcel increase the computation speed with little loss in accuracy. However, the MP-PIC method predicts an unphysical particle–particle overlap, which results in incorrect overall bed hydrodynamics. These results suggest using the CGHS method for fluidized bed...

Extension of a coarse grained particle method to simulate heat transfer in fluidized beds

The heat transfer in a gas-solids fluidized bed is simulated with computational fluid dynamic-discrete element method (CFD-DEM) and coarse grained particle method (CGPM). In CGPM fewer numerical particles and their collisions are tracked by lumping several real particles into a computational parcel. The assumption is that the real particles inside a coarse grained particle (CGP) are made from same species and share identical physical properties including density, diameter and temperature. The parcel-fluid convection term in CGPM is calculated using the same method as in DEM. For all other heat transfer mechanisms, we derive in this study mathematical expressions that relate the new heat transfer terms for CGPM to those traditionally derived in DEM. This newly derived CGPM model is verified and validated by comparing the results with CFD-DEM simulation results and experiment data. The numerical results compare well with experimental data for both hydrodynamics and temperature profiles. The proposed CGPM model can be used for fast and accurate simulations of heat transfer in large scale gas-solids fluidized beds.

Coarse-Grained-Particle Method for Simulation of Liquid–Solids Reacting Flows

A coarse-grained-particle method (CGPM) that tracks fewer particles and their collisions by lumping several real particles into computational parcels is developed. We demonstrate that the accuracy of CGPM can be improved by properly selecting interpolation schemes used to compute flow variables at particle and computational grid locations. The computational speed of CGPM was shown to be similar to that of a widely used and less accurate particle in cell method (PIC). Finally, a chemical reaction mechanism based on rare earth elements (REE) leaching from coal byproducts was implemented with CGPM to study the effects of several flow and design parameters on the leaching process. A counter-current reactor was studied and optimized to maximize the mass fraction of REE in the liquid solution. The CGPM can now be employed to cheaply and accurately solve industrial-scale problems containing millions of computational parcels.

Symmetry boundary condition in dissipative particle dynamics

Dissipative particle dynamics (DPD) is a coarse-grained particle method for modeling mesoscopic hydrodynamics. Most of the DPD simulations are carried out in 3D requiring remarkable computation time. For symmetric systems, this time can be reduced significantly by simulating only one half or one quarter of the systems. However, such simulations are not yet possible due to a lack of schemes to treat symmetric boundaries in DPD. In this study, we propose a numerical scheme for the implementation of the symmetric boundary condition (SBC) in both dissipative particle dynamics (DPD) and multibody dissipative particle dynamics (MDPD) using a combined ghost particles and specular reflection (CGPSR) method. We validate our scheme in four different configurations. The results demonstrate that our scheme can accurately reproduce the system properties, such as velocity, density and meniscus shapes of a full system with numerical simulations of a subsystem. Using a symmetric boundary condition for one half of the system, we demonstrate about 50% computation time saving in both DPD and MDPD. This approach for symmetric boundary treatment can be also applied to other coarse-grained particle methods such as Brownian and Langevin Dynamics to significantly reduce computation time.

Development and Implementation of Recursive Coarse-Grained Particle Method for Meso-Scale Simulation

A coarse-graining method has been proposed [R. E. Rudd and J. Q. Broughton: Phys. Rev. B 58 (1998) R5893-R5896] for a crystalline system of atoms, in which the inter-particle interaction is obtained through coarse-graining of the partition function of the atomic Hamiltonian in the harmonic approximation. Though the method has attractive features such as its natural incorporation of atomistic phonons, the original formulation limits its application to small periodic systems without surfaces. In this paper, we improve the method as follows: (i) we introduce a recursive coarse-graining procedure to overcome the size limitation problem, (ii) we rewrite the deformation energy in both translation and rotation invariant form to make it applicable to macroscopically deformed systems, (iii) we extend the formulation for multi-component systems, and (iv) we incorporate the thermal expansion and softening of the atomistic systems. The essentials in the code implementation are explained. The method is successfully applied to deforming nanorods of sub-micron size in both two and three dimensions, to show that it is ready for dynamics simulation of meso-scale, three-dimensional realistic systems.

材料計算における粗視化法の新たな展開 : 擬連続体法と粗視化粒子法(計算力学・工学におけるマルチスケールモデリング,<特集>理学と工学,科学と技術をつなぐマルチスケールモデリング)

材料計算における粗視化法の新たな展開 : 擬連続体法と粗視化粒子法(計算力学・工学におけるマルチスケールモデリング,<特集>理学と工学,科学と技術をつなぐマルチスケールモデリング)