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Title: Large scale Brownian dynamics of confined suspensions of rigid particles

Abstract

We introduce methods for large-scale Brownian Dynamics (BD) simulation of many rigid particles of arbitrary shape suspended in a fluctuating fluid. Our method adds Brownian motion to the rigid multiblob method [F. Balboa Usabiaga et al., Commun. Appl. Math. Comput. Sci. 11(2), 217–296 (2016)] at a cost comparable to the cost of deterministic simulations. We demonstrate that we can efficiently generate deterministic and random displacements for many particles using preconditioned Krylov iterative methods, if kernel methods to efficiently compute the action of the Rotne-Prager-Yamakawa (RPY) mobility matrix and its “square” root are available for the given boundary conditions. These kernel operations can be computed with near linear scaling for periodic domains using the positively split Ewald method. Here we study particles partially confined by gravity above a no-slip bottom wall using a graphical processing unit implementation of the mobility matrix-vector product, combined with a preconditioned Lanczos iteration for generating Brownian displacements. We address a major challenge in large-scale BD simulations, capturing the stochastic drift term that arises because of the configuration-dependent mobility. Unlike the widely used Fixman midpoint scheme, our methods utilize random finite differences and do not require the solution of resistance problems or the computation of the actionmore » of the inverse square root of the RPY mobility matrix. We construct two temporal schemes which are viable for large-scale simulations, an Euler-Maruyama traction scheme and a trapezoidal slip scheme, which minimize the number of mobility problems to be solved per time step while capturing the required stochastic drift terms. We validate and compare these schemes numerically by modeling suspensions of boomerang-shaped particles sedimented near a bottom wall. Using the trapezoidal scheme, we investigate the steady-state active motion in dense suspensions of confined microrollers, whose height above the wall is set by a combination of thermal noise and active flows. We find the existence of two populations of active particles, slower ones closer to the bottom and faster ones above them, and demonstrate that our method provides quantitative accuracy even with relatively coarse resolutions of the particle geometry.« less

Authors:
 [1]; ORCiD logo [2];  [1];  [3]
  1. Northwestern Univ., Evanston, IL (United States)
  2. New York Univ. (NYU), NY (United States); Simons Foundation, New York, NY (United States)
  3. New York Univ. (NYU), NY (United States)
Publication Date:
Research Org.:
New York Univ. (NYU), NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21)
OSTI Identifier:
1512935
Alternate Identifier(s):
OSTI ID: 1414609
Grant/Contract Number:  
SC0008271
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 147; Journal Issue: 24; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING

Citation Formats

Sprinkle, Brennan, Balboa Usabiaga, Florencio, Patankar, Neelesh A., and Donev, Aleksandar. Large scale Brownian dynamics of confined suspensions of rigid particles. United States: N. p., 2017. Web. doi:10.1063/1.5003833.
Sprinkle, Brennan, Balboa Usabiaga, Florencio, Patankar, Neelesh A., & Donev, Aleksandar. Large scale Brownian dynamics of confined suspensions of rigid particles. United States. doi:10.1063/1.5003833.
Sprinkle, Brennan, Balboa Usabiaga, Florencio, Patankar, Neelesh A., and Donev, Aleksandar. Fri . "Large scale Brownian dynamics of confined suspensions of rigid particles". United States. doi:10.1063/1.5003833. https://www.osti.gov/servlets/purl/1512935.
@article{osti_1512935,
title = {Large scale Brownian dynamics of confined suspensions of rigid particles},
author = {Sprinkle, Brennan and Balboa Usabiaga, Florencio and Patankar, Neelesh A. and Donev, Aleksandar},
abstractNote = {We introduce methods for large-scale Brownian Dynamics (BD) simulation of many rigid particles of arbitrary shape suspended in a fluctuating fluid. Our method adds Brownian motion to the rigid multiblob method [F. Balboa Usabiaga et al., Commun. Appl. Math. Comput. Sci. 11(2), 217–296 (2016)] at a cost comparable to the cost of deterministic simulations. We demonstrate that we can efficiently generate deterministic and random displacements for many particles using preconditioned Krylov iterative methods, if kernel methods to efficiently compute the action of the Rotne-Prager-Yamakawa (RPY) mobility matrix and its “square” root are available for the given boundary conditions. These kernel operations can be computed with near linear scaling for periodic domains using the positively split Ewald method. Here we study particles partially confined by gravity above a no-slip bottom wall using a graphical processing unit implementation of the mobility matrix-vector product, combined with a preconditioned Lanczos iteration for generating Brownian displacements. We address a major challenge in large-scale BD simulations, capturing the stochastic drift term that arises because of the configuration-dependent mobility. Unlike the widely used Fixman midpoint scheme, our methods utilize random finite differences and do not require the solution of resistance problems or the computation of the action of the inverse square root of the RPY mobility matrix. We construct two temporal schemes which are viable for large-scale simulations, an Euler-Maruyama traction scheme and a trapezoidal slip scheme, which minimize the number of mobility problems to be solved per time step while capturing the required stochastic drift terms. We validate and compare these schemes numerically by modeling suspensions of boomerang-shaped particles sedimented near a bottom wall. Using the trapezoidal scheme, we investigate the steady-state active motion in dense suspensions of confined microrollers, whose height above the wall is set by a combination of thermal noise and active flows. We find the existence of two populations of active particles, slower ones closer to the bottom and faster ones above them, and demonstrate that our method provides quantitative accuracy even with relatively coarse resolutions of the particle geometry.},
doi = {10.1063/1.5003833},
journal = {Journal of Chemical Physics},
number = 24,
volume = 147,
place = {United States},
year = {2017},
month = {12}
}

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