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Control of the aggregate structure of magnetic cubic particles in a quasi-2D suspension via both the strength and direction of an applied magnetic field (multi-particle collision dynamics simulations)

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MOLECULAR PHYSICS 2023年第21期121卷

作者： Satoh, Akira Okada, Kazuya Suzuki, Seiya Yamanouchi, Takeru Quadra, Rafael Futamura, Muneo Akita Prefectural Univ Dept Mech Engn Yurihonjo Japan Saitama Inst Technol Dept Mech Engn Fukaya Japan Akita Prefectural Univ Grad Sch Yurihonjo Japan

We have first investigated a feasibility of a malt-particle collision dynamics (MPCD) method by addressing whether or not the translational and rotational Brownian motion is activated at a physically reasonable level. From the results with respect to the root mean square velocities, we conclude that the MPCD method is a quite feasible simulation technique for a suspension composed of magnetic cubic particles. Then we have applied the MPCD simulation method to a quasi-2D system of magnetic cubic particles in order to control a regime change in the internal structure of particle aggregates by means of the strength and direction of a uniform applied magnetic field. In the case of a magnetic field applied in a certain direction from the 2D plane, a regime change in the internal structure of large densely-packed clusters into a regular configuration is more effectively attained than a magnetic field applied along the 2D plane.

关键词： Regime change magnetic cubic particle aggregation phenomenon cluster formation multi-particle collision dynamics

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Regime change in the aggregate structure of magnetic disk-like particles in a quasi-2D suspension system via multi-particle collision dynamics simulations*

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MOLECULAR PHYSICS 2022年第17期120卷 Article: e2109524页

作者： Satoh, Akira Akita Prefectural Univ Dept Mech Engn Yurihonjo Japan

We have addressed the problem of controlling a regime change in a quasi-2D system of magnetic disk-like particles by means of the strength and direction of an applied magnetic field. In the present study, two typical directions have been addressed, i.e. a y-direction field parallel to the 2D plane and a z-direction field normal to that plane of the particle disk. It is shown that the direction of an applied magnetic field is a significant factor in particle aggregation and can give rise to different regime changes. That is, an applied magnetic field parallel to the 2D system plane functions to induce a regime change in the aggregate structure from linear column-like particle clusters into a knitting-pattern formation, whereas in the case of an applied field normal to the 2D plane, a regime of long column-like clusters transforms into a particle distribution with no discernible internal structure.

关键词： Regime change magnetic disk-like particle aggregation phenomenon cluster formation multi-particle collision dynamics

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A Trefoil Knot Polymer Chain Translocates through a Funnel-like Channel: A multi-particle collision dynamics Study

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POLYMERS 2022年第6期14卷 1164页

作者： Wen, Xiaohui Wang, Deyin Tang, Jiajun Yang, Zhiyong Chengdu Univ Technol Dept Phys Chengdu 610059 Peoples R China Jiangxi Agr Univ Dept Phys Nanchang 330045 Peoples R China

With combining multi-particle collision dynamics (MPCD) for the solvent and molecular dynamics (MD) for the polymer chains, we have studied the conformation and untying behaviors of a trefoil knot polymer chain translocated through a confined funnel-like channel. For the trefoil knot chain, we found that the untying knot behavior mostly happens during the translocation process, and the translocation behavior of linear chains is also simulated as a comparison. Some characteristics of the trefoil knot chain during translocation process, such as average gyration radius and the average end-to-end distances are discussed, and we statistic the scale relations of the translocation time versus the chain length, and that of the chain rigidity. This study may help to understand translocation behaviors of the knotted linear polymer chain in the capillary flow field.

关键词： trefoil knot chain solvent multi-particle collision dynamics funnel-like channel

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Feasibility of the multi-particle collision dynamics method as a simulation technique for a magnetic particle suspension

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MOLECULAR SIMULATION 2020年第3期46卷 213-223页

作者： Satoh, Akira Akita Prefectural Univ Dept Mech Engn Yurihonjo Japan

We have elucidated the feasibility of the multi-particle collision dynamics (MPCD) method as a technique for the simulation of a magnetic particle suspension, by addressing the dependence of the translational and rotational Brownian motion of the magnetic particles on the parameters that characterise a MPCD simulation. A reasonable level of activation of the Brownian motion is indispensable for simulating the aggregate structures of the magnetic particles because their internal structure is strongly dependent on particle Brownian motion. In the present study, we have employed a diffuse reflection model for treating the interaction between the fluid and the magnetic particles. The diffuse reflection model gives rise to the tendency that the translational Brownian motion of the magnetic particles is more significantly activated than the rotational Brownian motion. If a scaling coefficient is introduced for modifying the interaction between the fluid and the magnetic particles, a more accurate solution may be obtained in regard to the aggregate structures of the magnetic particles. We may conclude that the MPCD method with the diffuse reflection model is a promising simulation technique for analysing the behaviour of magnetic particles in a suspension.

关键词： Magnetic particle suspension multi-particle collision dynamics aggregation phenomenon Brownian motion pair correlation function

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Feasibility of multi-particle collision dynamics for rod-like particles and its application to a change in the orientational regime of a hematite particle suspension

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MOLECULAR PHYSICS 2021年第23期119卷 e1955987-e1955987页

作者： Yamanouchi, Takeru Cuadra, Rafael Satoh, Akira Akita Prefectural Univ Dept Mech Engn Yurihonjo Japan

We have verified that the method of multi-particle collision dynamics (MPCD) is able to activate a physically reasonable level of random motion in the medium of virtual fluid particles and activate the translational, ordinary rotational and spin rotational Brownian motion of the magnetic rod-like particles. MPCD was then applied to a quasi-2D system of rod-like hematite particles. The particle Brownian motion was found slightly over-activated, but this tendency decreased with smaller simulation time steps. The deviation from the theoretical value in the present results may be regarded to be acceptable as a first approximation since the Brownian motion was activated without the addition of any special technique. The applied magnetic field strength is found to play a significant role to enhance the order of the alignment of the raft-like clusters along the direction of the applied magnetic field. A similar orientational regime change along the applied magnetic field may be accomplished by an increase in the volumetric fraction of magnetic particles. We have therefore concluded that both an applied magnetic field and the particle volumetric fraction may be feasible parameters for inducing a regime change in the ordering of the orientation of rod-like hematite particles.

关键词： multi-particle collision dynamics magnetic rod-like particle hematite particle orientational regime change phase change

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Reactive multi-particle collision dynamics with reactive boundary conditions

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PHYSICAL BIOLOGY 2018年第4期15卷 046007-046007页

作者： Sayyidmousavi, Alireza Rohlf, Katrin Ryerson Univ Dept Math 350 Victoria St Toronto ON M5B 2K3 Canada

In the present study, an off-lattice particle-based method called the reactive multi-particle collision (RMPC) dynamics is extended to model reaction-diffusion systems with reactive boundary conditions in which the a priori diffusion coefficient of the particles needs to be maintained throughout the simulation. To this end, the authors have made use of the so-called bath particles whose purpose is only to ensure proper diffusion of the main particles in the system. In order to model partial adsorption by a reactive boundary in the RMPC, the probability of a particle being adsorbed, once it hits the boundary, is calculated by drawing an analogy between the RMPC and Brownian dynamics. The main advantages of the RMPC compared to other molecular based methods are less computational cost as well as conservation of mass, energy and momentum in the collision and free streaming steps. The proposed approach is tested on three reaction-diffusion systems and very good agreement with the solutions to their corresponding partial differential equations is observed.

关键词： multi-particle collision dynamics reactive boundary diffusion

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multi-particle collision dynamics simulation on capturing a target sphere fuelled by chemical reaction

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MOLECULAR PHYSICS 2016年第2期114卷 290-296页

作者： Gao, Tong Fan, Jia Tao, Yu-Guo Jilin Jianzhu Architecture Univ Sch Comp Sci & Engn Changchun Peoples R China Jilin Univ Hosp 2 Dept Neurol Changchun 130023 Peoples R China Univ Toronto Dept Chem Toronto ON M5S 1A1 Canada

The directed self-propulsion of a spherical target molecule fuelled by a chemical reaction is investigated. This source-target system consists of a spherical position-fixed source molecule and a freely moving target, separated at an initial distance R-0 in solution. The irreversible chemical reaction which converts A solvent particle to B species occurs catalytically on the surface of the source *** generates a non-equilibrium B solvent density gradient from the source to the target molecule. Therefore, a directed movement of the target can be achieved due to the difference of force between the target sphere and B solvent particles in all directions, and the target will finally be captured by the source. We have demonstrated the diffusiophoretic particle capture dynamics theoretically and described how the capture time and velocity can be affected by some key factors, such as chemical reaction rate, source and target molecule size, initial sphere separation, etc. The capture dynamics has also been studied by the coarse-grained mesoscopic hybrid molecular dynamics - multi-particle collision dynamics simulation. Great agreement has been found when we compare the simulated capture dynamics to the theoretical predictions. [GRAPHICS]

关键词： Molecular dynamics multi-particle collision dynamics chemical reaction diffusiophoretic density gradient

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Numerical simulation of star polymers under shear flow using a coupling method of multi-particle collision dynamics and molecular dynamics

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RHEOLOGICA ACTA 2015年第2期54卷 139-147页

作者： Yamamoto, Takehiro Masaoka, Norichika Osaka Univ Dept Mech Engn Suita Osaka 5650871 Japan

The numerical simulation of flow-induced structures is important for the flow analysis of complex fluids. Several schemes have been proposed for coupling the macro-flow computation and the microsimulation of the inner structure of complex fluids. In the present study, the flow-induced structure of star polymers was numerically simulated using a coupling method of multi-particle collision dynamics (MPCD) and coarse-grained molecular dynamics (MD). The polymers were modeled as elastic dumbbells, which consist of finitely extensible nonlinear elastic springs and beads. The motion of the beads was computed by MD. The MPCD was applied to model the effect of Brownian motion and hydrodynamic interactions among the beads. In the present study, the MPC-AT+a algorithm was employed for the collision steps in MPCD computations. The behavior of linear polymers in a shear flow was numerically analyzed to confirm the validity of the present simulation scheme. The numerical results agree well with both experimental results and predictions by other numerical methods. Furthermore, the simulation of star polymers under shear flow was carried out. The present simulation captured characteristic behaviors such as the configuration of the star polymers, which was more compact for polymers with more arms due to extruded volume effects, polymers tumbling at high Weissenberg numbers, and the fluctuation in expansions in the direction of flow decreasing for polymers with more arms.

关键词： multi-particle collision dynamics MPCD Flow-induced structures Star polymers Shear flows

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Flow simulations with multi-particle collision dynamics

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MECCANICA 2012年第8期47卷 2069-2077页

作者： De Angelis, E. Chinappi, M. Graziani, G. Univ Roma La Sapienza Dipartimento Ingn Meccan & Aerosp I-00184 Rome Italy Univ Bologna DIEM I-47100 Forli Italy Univ Roma La Sapienza Dipartimento Fis I-001185 Rome Italy

multi-particle collision dynamics (MPCD) is a particle based Navier-Stokes solver and in the last ten years it has been largely used to analyze mesoscopic systems where both hydrodynamics and thermal effects have to be taken into account, typical examples being colloidal suspensions and polymer solutions. Though the soundness of this approach is well documented, only a few studies present a systematic validation of the method as a Navier-Stokes solver for relatively complex flows (e.g. unsteady, non-uniform). In this study we use MPCD to simulate an unsteady periodic flow (second Stokes' problem) and a two dimensional flow (lid-driven cavity). Quantitative comparisons with analytical and finite difference results show that MPCD is able to correctly reproduce the hydrodynamics of these systems in a wide range of numerical parameter values, allowing the applications of MPCD to the analysis of complex fluids in confined geometries such as in Lab-On-a-Chip microfluidic devices. Discrepancies for certain parameter ranges and in specific flow conditions are singled out and discussed.

关键词： Computational methods in fluid dynamics multi-particle collision dynamics

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A hybrid method for micro-mesoscopic stochastic simulation of reaction-diffusion systems

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MATHEMATICAL BIOSCIENCES 2019年 312卷 23-32页

作者： Sayyidmousavi, Alireza Rohlf, Katrin Ilie, Silvana Ryerson Univ Dept Math 350 Victoria St Toronto ON M5B 2K3 Canada

The present paper introduces a new micro-meso hybrid algorithm based on the Ghost Cell Method concept in which the microscopic subdomain is governed by the Reactive multi-particle collision (RMPC) dynamics. The mesoscopic subdomain is modeled using the Reaction-Diffusion Master Equation (RDME). The RDME is solved by means of the Inhomogeneous Stochastic Simulation Algorithm. No hybrid algorithm has hitherto used the RMPC dynamics for modeling reactions and the trajectories of each individual particle. The RMPC is faster than other molecular based methods and has the advantage of conserving mass, energy and momentum in the collision and free streaming steps. The new algorithm is tested on three reaction-diffusion systems. In all the systems studied, very good agreement with the deterministic solutions of the corresponding differential equations is obtained. In addition, it has been shown that proper discretization of the computational domain results in significant speed-ups in comparison with the full RMPC algorithm.

关键词： Hybrid method Stochastic simulation multi-particle collision dynamics Inhomogeneous Stochastic Simulation Algorithm Reaction-diffusion systems

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