Brownian dynamics of confined suspensions of active microrollers

Balboa Usabiaga, Florencio; Delmotte, Blaise; Donev, Aleksandar

doi:10.1063/1.4979494

Title: Brownian dynamics of confined suspensions of active microrollers

Journal Article · Mon Apr 03 00:00:00 EDT 2017 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.4979494· OSTI ID:1465959

^[1]; Delmotte, Blaise ^[1]; Donev, Aleksandar ^[1]

New York Univ. (NYU), NY (United States). Courant Institute of Mathematical Sciences

In this study, we develop efficient numerical methods for performing many-body Brownian dynamics simulations of a recently observed fingering instability in an active suspension of colloidal rollers sedimented above a wall [M. Driscoll, B. Delmotte, M. Youssef, S. Sacanna, A. Donev, and P. Chaikin, Nat. Phys. (2016), preprint arXiv:1609.08673. We present a stochastic Adams-Bashforth integrator for the equations of Brownian dynamics, which has the same cost but is more accurate than the widely used Euler-Maruyama scheme, and use a random finite difference to capture the stochastic drift proportional to the divergence of the configuration-dependent mobility matrix. We generate the Brownian increments using a Krylov method and show that for particles confined to remain in the vicinity of a no-slip wall by gravity or active flows, the number of iterations is independent of the number of particles. Our numerical experiments with active rollers show that the thermal fluctuations set the characteristic height of the colloids above the wall, both in the initial condition and the subsequent evolution dominated by active flows. Finally, the characteristic height in turn controls the time scale and wavelength for the development of the fingering instability

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Research Organization:: New York Univ. (NYU), NY (United States). Courant Institute of Mathematical Sciences

Sponsoring Organization:: USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR). Scientific Discovery through Advanced Computing (SciDAC)

Grant/Contract Number:: SC0008271

OSTI ID:: 1465959

Alternate ID(s):: OSTI ID: 1361804

Journal Information:: Journal of Chemical Physics, Vol. 146, Issue 13; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 23 works

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References (69)

Tracer trajectories and displacement due to a micro-swimmer near a surface Mathijssen, A. J. T. M.; Pushkin, D. O.; Yeomans, J. M. Journal of Fluid Mechanics, Vol. 773 https://doi.org/10.1017/jfm.2015.269	journal	May 2015
Simple and efficient representations for the fundamental solutions of Stokes flow in a half-space Gimbutas, Z.; Greengard, L.; Veerapaneni, S. Journal of Fluid Mechanics, Vol. 776 https://doi.org/10.1017/jfm.2015.302	journal	July 2015
A highly accurate boundary treatment for confined Stokes flow Marin, Oana; Gustavsson, Katarina; Tornberg, Anna-Karin Computers & Fluids, Vol. 66 https://doi.org/10.1016/j.compfluid.2012.06.008	journal	August 2012
Stokesian Dynamics Brady, J. F.; Bossis, G. Annual Review of Fluid Mechanics, Vol. 20, Issue 1 https://doi.org/10.1146/annurev.fl.20.010188.000551	journal	January 1988
Construction of Langevin forces in the simulation of hydrodynamic interaction Fixman, Marshall Macromolecules, Vol. 19, Issue 4 https://doi.org/10.1021/ma00158a043	journal	July 1986
Preconditioned Krylov Subspace Methods for Sampling Multivariate Gaussian Distributions Chow, Edmond; Saad, Yousef SIAM Journal on Scientific Computing, Vol. 36, Issue 2 https://doi.org/10.1137/130920587	journal	January 2014
A study of spermatozoan swimming stability near a surface Ishimoto, Kenta; Gaffney, Eamonn A. Journal of Theoretical Biology, Vol. 360 https://doi.org/10.1016/j.jtbi.2014.06.034	journal	November 2014
Dynamics of confined suspensions of swimming particles Hernandez-Ortiz, Juan P.; Underhill, Patrick T.; Graham, Michael D. Journal of Physics: Condensed Matter, Vol. 21, Issue 20 https://doi.org/10.1088/0953-8984/21/20/204107	journal	April 2009
Fluctuating force-coupling method for simulations of colloidal suspensions Keaveny, Eric E. Journal of Computational Physics, Vol. 269 https://doi.org/10.1016/j.jcp.2014.03.013	journal	July 2014
Short-Time Dynamics in Quasi-Two-Dimensional Colloidal Suspensions Santana-Solano, Jesús; Ramírez-Saito, Angeles; Arauz-Lara, José Luis Physical Review Letters, Vol. 95, Issue 19 https://doi.org/10.1103/physrevlett.95.198301	journal	October 2005
Impact of external flow on the dynamics of swimming microorganisms near surfaces Chilukuri, Sandeep; Collins, Cynthia H.; Underhill, Patrick T. Journal of Physics: Condensed Matter, Vol. 26, Issue 11 https://doi.org/10.1088/0953-8984/26/11/115101	journal	March 2014
Improvement of the Stokesian Dynamics method for systems with a finite number of particles Ichiki, Kengo Journal of Fluid Mechanics, Vol. 452 https://doi.org/10.1017/s0022112001006735	journal	February 2002
An immersed boundary method for rigid bodies Kallemov, Bakytzhan; Bhalla, Amneet; Griffith, Boyce Communications in Applied Mathematics and Computational Science, Vol. 11, Issue 1 https://doi.org/10.2140/camcos.2016.11.79	journal	January 2016
Many-body microhydrodynamics of colloidal particles with active boundary layers Singh, Rajesh; Ghose, Somdeb; Adhikari, R. Journal of Statistical Mechanics: Theory and Experiment, Vol. 2015, Issue 6 https://doi.org/10.1088/1742-5468/2015/06/p06017	journal	June 2015
Boundaries can steer active Janus spheres Das, Sambeeta; Garg, Astha; Campbell, Andrew I. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9999	journal	December 2015
Hydrodynamic interactions in long chain polymers: Application of the Chebyshev polynomial approximation in stochastic simulations Jendrejack, Richard M.; Graham, Michael D.; de Pablo, Juan J. The Journal of Chemical Physics, Vol. 113, Issue 7 https://doi.org/10.1063/1.1305884	journal	August 2000
Hydrodynamic Attraction of Swimming Microorganisms by Surfaces Berke, Allison P.; Turner, Linda; Berg, Howard C. Physical Review Letters, Vol. 101, Issue 3 https://doi.org/10.1103/physrevlett.101.038102	journal	July 2008
Hydrodynamic capture of microswimmers into sphere-bound orbits Takagi, Daisuke; Palacci, Jérémie; Braunschweig, Adam B. Soft Matter, Vol. 10, Issue 11 https://doi.org/10.1039/c3sm52815d	journal	January 2014
Dynamic self-assembly of microscale rotors and swimmers Davies Wykes, Megan S.; Palacci, Jérémie; Adachi, Takuji Soft Matter, Vol. 12, Issue 20 https://doi.org/10.1039/c5sm03127c	journal	January 2016
Generalization of the Rotne–Prager–Yamakawa mobility and shear disturbance tensors Wajnryb, Eligiusz; Mizerski, Krzysztof A.; Zuk, Pawel J. Journal of Fluid Mechanics, Vol. 731 https://doi.org/10.1017/jfm.2013.402	journal	August 2013
A fast multipole method for the Rotne–Prager–Yamakawa tensor and its applications Liang, Zhi; Gimbutas, Zydrunas; Greengard, Leslie Journal of Computational Physics, Vol. 234 https://doi.org/10.1016/j.jcp.2012.09.021	journal	February 2013
Dynamic simulation of hydrodynamically interacting particles Durlofsky, L.; Brady, J. F.; Bossis, G. Journal of Fluid Mechanics, Vol. 180, Issue -1 https://doi.org/10.1017/s002211208700171x	journal	July 1987
Hydrodynamics of suspensions of passive and active rigid particles: a rigid multiblob approach Balboa Usabiaga, Florencio; Kallemov, Bakytzhan; Delmotte, Blaise Communications in Applied Mathematics and Computational Science, Vol. 11, Issue 2 https://doi.org/10.2140/camcos.2016.11.217	journal	January 2016
Rapid sampling of stochastic displacements in Brownian dynamics simulations Fiore, Andrew M.; Balboa Usabiaga, Florencio; Donev, Aleksandar The Journal of Chemical Physics, Vol. 146, Issue 12 https://doi.org/10.1063/1.4978242	journal	March 2017
Weak Second Order Explicit Stabilized Methods for Stiff Stochastic Differential Equations Abdulle, Assyr; Vilmart, Gilles; Zygalakis, Konstantinos C. SIAM Journal on Scientific Computing, Vol. 35, Issue 4 https://doi.org/10.1137/12088954x	journal	January 2013
Colloidal diffusion and hydrodynamic screening near boundaries Lele, Pushkar P.; Swan, James W.; Brady, John F. Soft Matter, Vol. 7, Issue 15 https://doi.org/10.1039/c0sm01466d	journal	January 2011
Brownian Motion of Boomerang Colloidal Particles Chakrabarty, Ayan; Konya, Andrew; Wang, Feng Physical Review Letters, Vol. 111, Issue 16 https://doi.org/10.1103/physrevlett.111.160603	journal	October 2013
Simulation of polymer dynamics. I. General theory Fixman, Marshall The Journal of Chemical Physics, Vol. 69, Issue 4 https://doi.org/10.1063/1.436725	journal	August 1978
Dynamics of Concentrated Hard-Sphere Colloids Near a Wall Michailidou, V. N.; Petekidis, G.; Swan, J. W. Physical Review Letters, Vol. 102, Issue 6 https://doi.org/10.1103/physrevlett.102.068302	journal	February 2009
PyCUDA and PyOpenCL: A scripting-based approach to GPU run-time code generation Klöckner, Andreas; Pinto, Nicolas; Lee, Yunsup Parallel Computing, Vol. 38, Issue 3 https://doi.org/10.1016/j.parco.2011.09.001	journal	March 2012
Brownian dynamics close to a wall studied by photon correlation spectroscopy from an evanescent wave Lan, K. H.; Ostrowsky, N.; Sornette, D. Physical Review Letters, Vol. 57, Issue 1 https://doi.org/10.1103/physrevlett.57.17	journal	July 1986
Brownian dynamics without Green's functions Delong, Steven; Usabiaga, Florencio Balboa; Delgado-Buscalioni, Rafael The Journal of Chemical Physics, Vol. 140, Issue 13 https://doi.org/10.1063/1.4869866	journal	April 2014
Simulating Brownian suspensions with fluctuating hydrodynamics Delmotte, Blaise; Keaveny, Eric E. The Journal of Chemical Physics, Vol. 143, Issue 24 https://doi.org/10.1063/1.4938173	journal	December 2015
Rapid calculation of hydrodynamic and transport properties in concentrated solutions of colloidal particles and macromolecules Swan, James W.; Wang, Gang Physics of Fluids, Vol. 28, Issue 1 https://doi.org/10.1063/1.4939581	journal	January 2016
Periodic and Chaotic Orbits of Plane-Confined Micro-rotors in Creeping Flows Lushi, Enkeleida; Vlahovska, Petia M. Journal of Nonlinear Science, Vol. 25, Issue 5 https://doi.org/10.1007/s00332-015-9254-9	journal	April 2015
Simulation of hydrodynamically interacting particles near a no-slip boundary Swan, James W.; Brady, John F. Physics of Fluids, Vol. 19, Issue 11 https://doi.org/10.1063/1.2803837	journal	November 2007
Finding the ciliary beating pattern with optimal efficiency Osterman, N.; Vilfan, A. Proceedings of the National Academy of Sciences, Vol. 108, Issue 38 https://doi.org/10.1073/pnas.1107889108	journal	September 2011
Numerical integration of stochastic differential equations: weak second-order mid-point scheme for application in the composition PDF method Cao, Renfeng; Pope, Stephen B. Journal of Computational Physics, Vol. 185, Issue 1 https://doi.org/10.1016/s0021-9991(02)00054-2	journal	February 2003
Living Crystals of Light-Activated Colloidal Surfers Palacci, J.; Sacanna, S.; Steinberg, A. P. Science, Vol. 339, Issue 6122 https://doi.org/10.1126/science.1230020	journal	January 2013
Universal Hydrodynamic Mechanisms for Crystallization in Active Colloidal Suspensions Singh, Rajesh; Adhikari, R. Physical Review Letters, Vol. 117, Issue 22 https://doi.org/10.1103/physrevlett.117.228002	journal	November 2016
Hydrodynamic Interaction in Confined Geometries Diamant, Haim Journal of the Physical Society of Japan, Vol. 78, Issue 4 https://doi.org/10.1143/jpsj.78.041002	journal	April 2009
Magnetic Click Colloidal Assembly Sacanna, Stefano; Rossi, Laura; Pine, David J. Journal of the American Chemical Society, Vol. 134, Issue 14 https://doi.org/10.1021/ja301344n	journal	March 2012
Accelerated Stokesian dynamics: Brownian motion Banchio, Adolfo J.; Brady, John F. The Journal of Chemical Physics, Vol. 118, Issue 22 https://doi.org/10.1063/1.1571819	journal	June 2003
Fast Ewald summation for Stokesian particle suspensions: FAST EWALD SUMMATION FOR STOKESIAN PARTICLE SUSPENSIONS Af Klinteberg, Ludvig; Tornberg, Anna-Karin International Journal for Numerical Methods in Fluids, Vol. 76, Issue 10 https://doi.org/10.1002/fld.3953	journal	September 2014
Unstable fronts and motile structures formed by microrollers Driscoll, Michelle; Delmotte, Blaise; Youssef, Mena Nature Physics, Vol. 13, Issue 4 https://doi.org/10.1038/nphys3970	journal	December 2016
Hydrodynamics of self-propulsion near a boundary: predictions and accuracy of far-field approximations Spagnolie, Saverio E.; Lauga, Eric Journal of Fluid Mechanics, Vol. 700 https://doi.org/10.1017/jfm.2012.101	journal	April 2012
Particle motion between parallel walls: Hydrodynamics and simulation Swan, James W.; Brady, John F. Physics of Fluids, Vol. 22, Issue 10 https://doi.org/10.1063/1.3487748	journal	October 2010
Metropolis Integration Schemes for Self-Adjoint Diffusions Bou-Rabee, Nawaf; Donev, Aleksandar; Vanden-Eijnden, Eric Multiscale Modeling & Simulation, Vol. 12, Issue 2 https://doi.org/10.1137/130937470	journal	January 2014
Computation of the singular and regularized image systems for doubly-periodic Stokes flow in the presence of a wall Nguyen, Hoang-Ngan; Leiderman, Karin Journal of Computational Physics, Vol. 297 https://doi.org/10.1016/j.jcp.2015.05.030	journal	September 2015
Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations Ando, Tadashi; Chow, Edmond; Saad, Yousef The Journal of Chemical Physics, Vol. 137, Issue 6 https://doi.org/10.1063/1.4742347	journal	August 2012
Brownian dynamics of confined rigid bodies Delong, Steven; Balboa Usabiaga, Florencio; Donev, Aleksandar The Journal of Chemical Physics, Vol. 143, Issue 14 https://doi.org/10.1063/1.4932062	journal	October 2015
Variational Treatment of Hydrodynamic Interaction in Polymers Rotne, Jens; Prager, Stephen The Journal of Chemical Physics, Vol. 50, Issue 11 https://doi.org/10.1063/1.1670977	journal	June 1969
GPU-accelerated simulation of colloidal suspensions with direct hydrodynamic interactions Kopp, M.; Höfling, F. The European Physical Journal Special Topics, Vol. 210, Issue 1 https://doi.org/10.1140/epjst/e2012-01640-1	journal	August 2012
Dynamic self-assembly of microscale rotors and swimmers. Davies Wykes, Megan; Palacci, Jérémie; Adachi, Takuji Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.34101	text	January 2016
An immersed boundary method for rigid bodies Singh, Bhalla, Amneet Pal; Aleksandar, Donev,; Bakytzhan, Kallemov, The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/4r5d-6f46	text	January 2016
Hydrodynamics of suspensions of passive and active rigid particles: a rigid multiblob approach Balboa, Usabiaga, Florencio; Singh, Bhalla, Amneet Pal; Bakytzhan, Kallemov, The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/schb-ht77	text	January 2016
Hydrodynamic interaction in confined geometries Diamant, Haim arXiv https://doi.org/10.48550/arxiv.0812.4971	text	January 2008
PyCUDA and PyOpenCL: A Scripting-Based Approach to GPU Run-Time Code Generation Klöckner, Andreas; Pinto, Nicolas; Lee, Yunsup arXiv https://doi.org/10.48550/arxiv.0911.3456	text	January 2009
GPU-accelerated simulation of colloidal suspensions with direct hydrodynamic interactions Kopp, Michael; Höfling, Felix arXiv https://doi.org/10.48550/arxiv.1205.6333	text	January 2012
Generalization of the Rotne-Prager-Yamakawa mobility and shear disturbance tensors Wajnryb, Eligiusz; Mizerski, Krzysztof A.; Zuk, Pawel J. arXiv https://doi.org/10.48550/arxiv.1307.7312	text	January 2013
Collective dynamics in a binary mixture of hydrodynamically coupled micro-rotors Yeo, Kyongmin; Lushi, Enkeleida; Vlahovska, Petia M. arXiv https://doi.org/10.48550/arxiv.1410.2878	text	January 2014
Many-body microhydrodynamics of colloidal particles with active boundary layers Singh, Rajesh; Ghose, Somdeb; Adhikari, R. arXiv https://doi.org/10.48550/arxiv.1411.0278	text	January 2014
Periodic and chaotic orbits of plane-confined micro-rotors in creeping flows Lushi, Enkeleida; Vlahovska, Petia M. arXiv https://doi.org/10.48550/arxiv.1503.01805	text	January 2015
Simple and efficient representations for the fundamental solutions of Stokes flow in a half-space Gimbutas, Zydrunas; Greengard, Leslie; Veerapaneni, Shravan arXiv https://doi.org/10.48550/arxiv.1504.00102	preprint	January 2015
Simulating Brownian suspensions with fluctuating hydrodynamics Delmotte, Blaise; Keaveny, Eric E. arXiv https://doi.org/10.48550/arxiv.1507.02185	text	January 2015
Rapid Sampling of Stochastic Displacements in Brownian Dynamics Simulations Fiore, A. M.; Usabiaga, F. Balboa; Donev, A. arXiv https://doi.org/10.48550/arxiv.1611.09322	text	January 2016
Simulation of polymer dynamics. II. Relaxation rates and dynamic viscosity Fixman, Marshall The Journal of Chemical Physics, Vol. 69, Issue 4 https://doi.org/10.1063/1.436726	journal	August 1978
Fluctuating force-coupling method for simulations of colloidal suspensions Keaveny, Eric E. arXiv https://doi.org/10.48550/arxiv.1306.1706	text	January 2013
Peer reviews of "Interdisciplinary, interinstitutional and international collaboration of family medicine researchers in Taiwan" Version 0.2 PeerJ https://doi.org/10.7287/peerj.1321v0.2/reviews/2	posted_content	September 2015

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