Table of Content

01 January 2018, Volume 39 Issue 1

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Articles

Preface: theory, methods, and applications of mesoscopic modeling

Z. LI, Guohui HU, G. E. KARNIADAKIS

2018, 39(1):  1-2.  doi:10.1007/s10483-018-2260-6

Abstract ( 436 )   HTML   PDF (60KB) ( 484 )  

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Modeling biomembranes and red blood cells by coarse-grained particle methods

H. LI, H. Y. CHANG, J. YANG, L. LU, Y. H. TANG, G. LYKOTRAFITIS

2018, 39(1):  3-20.  doi:10.1007/s10483-018-2252-6

Abstract ( 440 )   HTML   PDF (3145KB) ( 316 )  

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In this work, the previously developed coarse-grained (CG) particle models for biomembranes and red blood cells (RBCs) are reviewed, and the advantages of the CG particle methods over the continuum and atomistic simulations for modeling biological phenomena are discussed. CG particle models can largely increase the length scale and time scale of atomistic simulations by eliminating the fast degrees of freedom while preserving the mesoscopic structures and properties of the simulated system. Moreover, CG particle models can be used to capture the microstructural alternations in diseased RBCs and simulate the topological changes of biomembranes and RBCs, which are the major challenges to the typical continuum representations of membranes and RBCs. The power and versatility of CG particle methods are demonstrated through simulating the dynamical processes involving significant topological changes, e.g., lipid self-assembly vesicle fusion and membrane budding.

Lattice Boltzmann simulations of high-order statistics in isotropic turbulent flows

Guodong JIN, Shizhao WANG, Yun WANG, Guowei HE

2018, 39(1):  21-30.  doi:10.1007/s10483-018-2254-9

Abstract ( 479 )   HTML   PDF (360KB) ( 189 )  

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The lattice Boltzmann method (LBM) is coupled with the multiple-relaxationtime (MRT) collision model and the three-dimensional 19-discrete-velocity (D3Q19) model to resolve intermittent behaviors on small scales in isotropic turbulent flows. The highorder scaling exponents of the velocity structure functions, the probability distribution functions of Lagrangian accelerations, and the local energy dissipation rates are investigated. The self-similarity of the space-time velocity structure functions is explored using the extended self-similarity (ESS) method, which was originally developed for velocity spatial structure functions. The scaling exponents of spatial structure functions at up to ten orders are consistent with the experimental measurements and theoretical results, implying that the LBM can accurately resolve the intermittent behaviors. This validation provides a solid basis for using the LBM to study more complex processes that are sensitive to small scales in turbulent flows, such as the relative dispersion of pollutants and mesoscale structures of preferential concentration of heavy particles suspended in turbulent flows.

Discussions on the correspondence of dissipative particle dynamics and Langevin dynamics at small scales

D. AZARNYKH, S. LITVINOV, X. BIAN, N. A. ADAMS

2018, 39(1):  31-46.  doi:10.1007/s10483-018-2258-9

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We investigate the behavior of dissipative particle dynamics (DPD) within different scaling regimes by numerical simulations. The paper extends earlier analytical findings of Ripoll, M., Ernst, M. H., and Español, P. (Large scale and mesoscopic hydrodynamics for dissipative particle dynamics. Journal of Chemical Physics, 115(15), 7271-7281 (2001)) by evaluation of numerical data for the particle and collective scaling regimes and the four different subregimes. DPD simulations are performed for a range of dynamic overlapping parameters. Based on analyses of the current auto-correlation functions (CACFs), we demonstrate that within the particle regime at scales smaller than its force cut-off radius, DPD follows Langevin dynamics. For the collective regime, we show that the small-scale behavior of DPD differs from Langevin dynamics. For the wavenumber-dependent effective shear viscosity, universal scaling regimes are observed in the microscopic and mesoscopic wavenumber ranges over the considered range of dynamic overlapping parameters.

Mesoscale modeling of microgel mechanics and kinetics through the swelling transition

S. NIKOLOV, A. FERNANDEZ-NIEVES, A. ALEXEEV

2018, 39(1):  47-62.  doi:10.1007/s10483-018-2259-6

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The mechanics and swelling kinetics of polymeric microgels are simulated using a mesoscale computational model based on dissipative particle dynamics. Microgels are represented by a random elastic network submerged in an explicit viscous solvent. The model is used to probe the effect of different solvent conditions on the bulk modulus of the microgels. Comparison of the simulation results through the volume phase transition reveals favorable agreement with Flory-Rehner's theory for polymeric gels. The model is also used to examine the microgel swelling kinetics, and is found to be in good agreement with Tanaka's theory for spherical gels. The simulations show that, during the swelling process, the microgel maintains a nearly homogeneous structure, whereas deswelling is characterized by the formation of chain bundles and network coarsening.

A note on hydrodynamics from dissipative particle dynamics

X. BIAN, Z. LI, N. A. ADAMS

2018, 39(1):  63-82.  doi:10.1007/s10483-018-2257-9

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We calculate current correlation functions (CCFs) of dissipative particle dynamics (DPD) and compare them with results of molecular dynamics (MD) and solutions of linearized hydrodynamic equations. In particular, we consider three versions of DPD, the empirical/classical DPD, coarse-grained (CG) DPD with radial-direction interactions only and full (radial, transversal, and rotational) interactions between particles. To facilitate quantitative discussions, we consider specifically a star-polymer melt system at a moderate density. For bonded molecules, it is straightforward to define the CG variables and to further derive CG force fields for DPD within the framework of the Mori-Zwanzig formalism. For both transversal and longitudinal current correlation functions (TCCFs and LCCFs), we observe that results of MD, DPD, and hydrodynamic solutions agree with each other at the continuum limit. Below the continuum limit to certain length scales, results of MD deviate significantly from hydrodynamic solutions, whereas results of both empirical and CG DPD resemble those of MD. This indicates that the DPD method with Markovian force laws possibly has a larger applicability than the continuum description of a Newtonian fluid. This is worth being explored further to represent generalized hydrodynamics.

Stable and accurate schemes for smoothed dissipative particle dynamics

G. FAURE, G. STOLTZ

2018, 39(1):  83-102.  doi:10.1007/s10483-018-2256-8

Abstract ( 398 )   HTML   PDF (551KB) ( 107 )  

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Smoothed dissipative particle dynamics (SDPD) is a mesoscopic particle method that allows to select the level of resolution at which a fluid is simulated. The numerical integration of its equations of motion still suffers from the lack of numerical schemes satisfying all the desired properties such as energy conservation and stability. Similarities between SDPD and dissipative particle dynamics with energy (DPDE) conservation, which is another coarse-grained model, enable adaptation of recent numerical schemes developed for DPDE to the SDPD setting. In this article, a Metropolis step in the integration of the fluctuation/dissipation part of SDPD is introduced to improve its stability.

Everything you always wanted to know about SDPD^* (^*but were afraid to ask)

M. ELLERO, P. ESPAÑOL

2018, 39(1):  103-124.  doi:10.1007/s10483-018-2255-6

Abstract ( 491 )   HTML   PDF (501KB) ( 188 )  

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An overview of the smoothed dissipative particle dynamics (SDPD) method is presented in a format that tries to quickly answer questions that often arise among users and newcomers. It is hoped that the status of SDPD is clarified as a mesoscopic particle model and its potentials and limitations are highlighted, as compared with other methods.

Fluctuating hydrodynamic methods for fluid-structure interactions in confined channel geometries

Y. WANG, H. LEI, P. J. ATZBERGER

2018, 39(1):  125-152.  doi:10.1007/s10483-018-2253-8

Abstract ( 468 )   HTML   PDF (2777KB) ( 143 )  

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We develop computational methods for the study of fluid-structure interactions subject to thermal fluctuations when confined within channels with slit-like geometry. The methods take into account the hydrodynamic coupling and diffusivity of microstructures when influenced by their proximity to no-slip walls. We develop stochastic numerical methods subject to no-slip boundary conditions using a staggered finite volume discretization. We introduce techniques for discretizing stochastic systems in a manner that ensures results consistent with statistical mechanics. We show how an exact fluctuation-dissipation condition can be used for this purpose to discretize the stochastic driving fields and combined with an exact projection method to enforce incompressibility. We demonstrate our computational methods by investigating how the proximity of ellipsoidal colloids to the channel wall affects their active hydrodynamic responses and passive diffusivity. We also study for a large number of interacting particles collective drift-diffusion dynamics and associated correlation functions. We expect the introduced stochastic computational methods to be broadly applicable to applications in which confinement effects play an important role in the dynamics of microstructures subject to hydrodynamic coupling and thermal fluctuations.