1
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Bailey MR, Barriuso Gutiérrez CM, Martín-Roca J, Niggel V, Carrasco-Fadanelli V, Buttinoni I, Pagonabarraga I, Isa L, Valeriani C. Minimal numerical ingredients describe chemical microswimmers' 3-D motion. NANOSCALE 2024; 16:2444-2451. [PMID: 38214073 DOI: 10.1039/d3nr03695b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
The underlying mechanisms and physics of catalytic Janus microswimmers is highly complex, requiring details of the associated phoretic fields and the physiochemical properties of catalyst, particle, boundaries, and the fuel used. Therefore, developing a minimal (and more general) model capable of capturing the overall dynamics of these autonomous particles is highly desirable. In the presented work, we demonstrate that a coarse-grained dissipative particle-hydrodynamics model is capable of describing the behaviour of various chemical microswimmer systems. Specifically, we show how a competing balance between hydrodynamic interactions experienced by a squirmer in the presence of a substrate, gravity, and mass and shape asymmetries can reproduce a range of dynamics seen in different experimental systems. We hope that our general model will inspire further synthetic work where various modes of swimmer motion can be encoded via shape and mass during fabrication, helping to realise the still outstanding goal of microswimmers capable of complex 3-D behaviour.
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Affiliation(s)
- Maximilian R Bailey
- Laboratory for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Zürich, Switzerland
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Madrid, Spain.
| | - C Miguel Barriuso Gutiérrez
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Madrid, Spain.
| | - José Martín-Roca
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Madrid, Spain.
- Departamento de Química Física, Facultad de Química, Universidad Complutense de Madrid, Madrid, Spain
| | - Vincent Niggel
- Laboratory for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Virginia Carrasco-Fadanelli
- Department of Physics, Institute of Experimental Colloidal Physics, Heinrich-Heine University, Düsseldorf, Germany
| | - Ivo Buttinoni
- Department of Physics, Institute of Experimental Colloidal Physics, Heinrich-Heine University, Düsseldorf, Germany
| | - Ignacio Pagonabarraga
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, Barcelona, Spain
| | - Lucio Isa
- Laboratory for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Chantal Valeriani
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Madrid, Spain.
- GISC - Grupo Interdiplinar de Sistemas Complejos, Madrid, Spain
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2
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Potisk T, Sablić J, Svenšek D, Diego ES, Teran FJ, Praprotnik M. Analyte‐Driven Clustering of Bio‐Conjugated Magnetic Nanoparticles. ADVANCED THEORY AND SIMULATIONS 2023. [DOI: 10.1002/adts.202200796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Affiliation(s)
- Tilen Potisk
- Laboratory for Molecular Modeling National Institute of Chemistry SI‐1001 Ljubljana Slovenia
- Faculty of Mathematics and Physics University of Ljubljana SI‐1001 Ljubljana Slovenia
| | - Jurij Sablić
- Laboratory for Molecular Modeling National Institute of Chemistry SI‐1001 Ljubljana Slovenia
- Department of Condensed Matter Physics University of Barcelona E‐08028 Barcelona Spain
- Centre Européen de Calcul Atomique et Moléculaire École Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Daniel Svenšek
- Laboratory for Molecular Modeling National Institute of Chemistry SI‐1001 Ljubljana Slovenia
- Faculty of Mathematics and Physics University of Ljubljana SI‐1001 Ljubljana Slovenia
| | | | - Francisco J. Teran
- IMDEA Nanociencia Ciudad Universitaria de Cantoblanco 28049 Madrid Spain
- Nanobiotecnología (iMdea‐Nanociencia) Unidad Asociada al Centro Nacional de Biotecnología (CSIC) 28049 Madrid Spain
| | - Matej Praprotnik
- Laboratory for Molecular Modeling National Institute of Chemistry SI‐1001 Ljubljana Slovenia
- Faculty of Mathematics and Physics University of Ljubljana SI‐1001 Ljubljana Slovenia
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3
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Kreissl P, Holm C, Weeber R. Interplay between steric and hydrodynamic interactions for ellipsoidal magnetic nanoparticles in a polymer suspension. SOFT MATTER 2023; 19:1186-1193. [PMID: 36655681 DOI: 10.1039/d2sm01428a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Magnetic nanoparticles couple to polymeric environments by several mechanisms. These include van der Waals, steric, hydrodynamic and electrostatic forces. This leads to numerous interesting effects and potential applications. Still, the details of the coupling are often unknown. In a previous work, we showed that, for spherical particles, hydrodynamic coupling alone can explain experimentally observed trends in magnetic AC susceptibility spectra [P. Kreissl, C. Holm and R. Weeber, Soft Matter, 2021, 17, 174-183]. Non-spherical, elongated particles are of interest because an enhanced coupling to the surrounding polymers is expected. In this publication we study the interplay of steric and hydrodynamic interactions between those particles and a polymer suspension. To this end, we obtain rotational friction coefficients, relaxation times for the magnetic moment, and AC susceptibility spectra, and compare these for simulations with and without hydrodynamic interactions considered. We show that, even if the particle is ellipsoidal, its hydrodynamic interactions with the surrounding polymers are much stronger than the steric ones due to the shape-anisotropy of the particle.
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Affiliation(s)
- Patrick Kreissl
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
| | - Rudolf Weeber
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
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4
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Shao L, Ma J, Prelesnik JL, Zhou Y, Nguyen M, Zhao M, Jenekhe SA, Kalinin SV, Ferguson AL, Pfaendtner J, Mundy CJ, De Yoreo JJ, Baneyx F, Chen CL. Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction. Chem Rev 2022; 122:17397-17478. [PMID: 36260695 DOI: 10.1021/acs.chemrev.2c00220] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature. Because hierarchy gives rise to unique properties and functions, many have sought inspiration from nature when designing and fabricating hierarchical matter. More and more, however, nature's own high-information content building blocks, proteins, peptides, and peptidomimetics, are being coopted to build hierarchy because the information that determines structure, function, and interfacial interactions can be readily encoded in these versatile macromolecules. Here, we take stock of recent progress in the rational design and characterization of hierarchical materials produced from high-information content blocks with a focus on stimuli-responsive and "smart" architectures. We also review advances in the use of computational simulations and data-driven predictions to shed light on how the side chain chemistry and conformational flexibility of macromolecular blocks drive the emergence of order and the acquisition of hierarchy and also on how ionic, solvent, and surface effects influence the outcomes of assembly. Continued progress in the above areas will ultimately usher in an era where an understanding of designed interactions, surface effects, and solution conditions can be harnessed to achieve predictive materials synthesis across scale and drive emergent phenomena in the self-assembly and reconfiguration of high-information content building blocks.
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Affiliation(s)
- Li Shao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jinrong Ma
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Jesse L Prelesnik
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yicheng Zhou
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Mary Nguyen
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mingfei Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Samson A Jenekhe
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sergei V Kalinin
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Jim Pfaendtner
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Christopher J Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - François Baneyx
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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5
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Mostarac D, Kantorovich SS. Rheology of a Nanopolymer Synthesized through Directional Assembly of DNA Nanochambers, for Magnetic Applications. Macromolecules 2022; 55:6462-6473. [PMID: 35966117 PMCID: PMC9367010 DOI: 10.1021/acs.macromol.2c00738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/09/2022] [Indexed: 11/29/2022]
Abstract
![]()
We present a numerical study of the effects of monomer
shape and
magnetic nature of colloids on the behavior of a single magnetic filament
subjected to the simultaneous action of shear flow and a stationary
external magnetic field perpendicular to the flow. We find that based
on the magnetic nature of monomers, magnetic filaments exhibit a completely
different phenomenology. Applying an external magnetic field strongly
inhibits tumbling only for filaments with ferromagnetic monomers.
Filament orientation with respect to the flow direction is in this
case independent of monomer shape. In contrast, reorientational dynamics
in filaments with superparamagnetic monomers are not inhibited by
applied magnetic fields, but enhanced. We find that the filaments
with spherical, superparamagnetic monomers, depending on the flow
and external magnetic field strength, assume semipersistent, collapsed,
coiled conformations, and their characteristic time of tumbling is
a function of field strength. However, external magnetic fields do
not affect the characteristic time of tumbling for filaments with
cubic, superparamagnetic monomers, but increase how often tumbling
occurs.
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Affiliation(s)
- Deniz Mostarac
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
- Research Platform MMM Mathematics-Magnetism-Materials, 1090 Vienna, Austria
| | - Sofia S. Kantorovich
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
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6
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Qiao L, Slater GW. Capture and translocation of a rod-like molecule by a nanopore: orientation, charge distribution and hydrodynamics. Phys Chem Chem Phys 2022; 24:6444-6452. [PMID: 35244666 DOI: 10.1039/d2cp00313a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate the translocation of rods with different charge distributions using hybrid Langevin dynamics and lattice Boltzmann (LD-LB) simulations. Electrostatic interactions are added to the system using the P3M algorithm to model the electrohydrodynamic interactions (EHI). We first examine the free-solution electrophoretic properties of rods with various charge distributions. Our translocation simulation results suggest that the order parameter is asymmetric during the capture and escape processes despite the symmetric electric field lines, while the impacts of the charge distribution on rod orientation are more significant during the capture process. The capture/threading/escape times are under the combined effects of charge screening, rod orientation, and charge distributions. We also show that the mean capture time of a rod is shorter when it is launched near the wall because rods tend to align along the wall and hence with the local field lines. Remarkably, the orientational capture radius we proposed previously for uniformly charged rods is still valid in the presence of EHI.
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Affiliation(s)
- Le Qiao
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
| | - Gary W Slater
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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7
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Qi X, Zhao Y, Lachowski K, Boese J, Cai Y, Dollar O, Hellner B, Pozzo L, Pfaendtner J, Chun J, Baneyx F, Mundy CJ. Predictive Theoretical Framework for Dynamic Control of Bioinspired Hybrid Nanoparticle Self-Assembly. ACS NANO 2022; 16:1919-1928. [PMID: 35073061 DOI: 10.1021/acsnano.1c04923] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
At-will tailoring of the formation and reconfiguration of hierarchical structures is a key goal of modern nanomaterial design. Bioinspired systems comprising biomacromolecules and inorganic nanoparticles have potential for new functional material structures. Yet, consequential challenges remain because we lack a detailed understanding of the temporal and spatial interplay between participants when it is mediated by fundamental physicochemical interactions over a wide range of scales. Motivated by a system in which silica nanoparticles are reversibly and repeatedly assembled using a homobifunctional solid-binding protein and single-unit pH changes under near-neutral solution conditions, we develop a theoretical framework where interactions at the molecular and macroscopic scales are rigorously coupled based on colloidal theory and atomistic molecular dynamics simulations. We integrate these interactions into a predictive coarse-grained model that captures the pH-dependent reversibility and accurately matches small-angle X-ray scattering experiments at collective scales. The framework lays a foundation to connect microscopic details with the macroscopic behavior of complex bioinspired material systems and to control their behavior through an understanding of both equilibrium and nonequilibrium characteristics.
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Affiliation(s)
- Xin Qi
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Yundi Zhao
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Kacper Lachowski
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Julia Boese
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Yifeng Cai
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Orion Dollar
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Brittney Hellner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Lilo Pozzo
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jaehun Chun
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Levich Institute and Department of Chemical Engineering, CUNY City College of New York, New York, New York 10031, United States
| | - François Baneyx
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Christopher J Mundy
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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8
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Wani YM, Kovakas PG, Nikoubashman A, Howard MP. Diffusion and sedimentation in colloidal suspensions using multiparticle collision dynamics with a discrete particle model. J Chem Phys 2022; 156:024901. [PMID: 35032985 DOI: 10.1063/5.0075002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study self-diffusion and sedimentation in colloidal suspensions of nearly hard spheres using the multiparticle collision dynamics simulation method for the solvent with a discrete mesh model for the colloidal particles (MD+MPCD). We cover colloid volume fractions from 0.01 to 0.40 and compare the MD+MPCD simulations to experimental data and Brownian dynamics simulations with free-draining hydrodynamics (BD) as well as pairwise far-field hydrodynamics described using the Rotne-Prager-Yamakawa mobility tensor (BD+RPY). The dynamics in MD+MPCD suggest that the colloidal particles are only partially coupled to the solvent at short times. However, the long-time self-diffusion coefficient in MD+MPCD is comparable to that in experiments, and the sedimentation coefficient in MD+MPCD is in good agreement with that in experiments and BD+RPY, suggesting that MD+MPCD gives a reasonable description of hydrodynamic interactions in colloidal suspensions. The discrete-particle MD+MPCD approach is convenient and readily extended to more complex shapes, and we determine the long-time self-diffusion coefficient in suspensions of nearly hard cubes to demonstrate its generality.
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Affiliation(s)
- Yashraj M Wani
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | | | - Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Michael P Howard
- Department of Chemical Engineering, Auburn University, Auburn, Alabama 36849, USA
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9
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10
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Kaiser M, Kantorovich SS. Flux and separation of magneto-active superballs in applied fields. Phys Chem Chem Phys 2021; 23:23827-23835. [PMID: 34647560 PMCID: PMC8549445 DOI: 10.1039/d1cp03343c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The term "active matter" describes a class of out-of-equilibrium systems, whose ability to transform environmental to kinetic energy is sought after in multiple fields of science. A challenge that still remains is to craft nanometer-sized active particles, whose motion can be efficiently directed by externally applied bio-noninvasive stimuli. Adding a magnetic component and therefore being able to direct the motion of active nanoparticles with an applied magnetic field is one of the promising solutions in the field. In this study, we employ molecular dynamics simulations to predict an external field-induced flow that arises in mixtures of magneto-active nanosized cubic and spherical particles with distinct mutual orientations between magnetization and propulsion. We explain why the flux of the suspended particles in the field direction does not only depend on the angle between the active force, driving a particle forward, and the orientation of its magnetization, but also on particle shape and inter-particle interactions. Our results show that by tuning those parameters, one can achieve complete separation of particles according to their magnetization orientation. Based on our findings, along with optimizing the cargo properties of magneto-active nano-units, the actual composition of the magneto-active particle suspension can be characterized.
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Affiliation(s)
- Martin Kaiser
- University of Vienna, Physics Faculty/Research Platform MMM Mathematics-Magnetism-Materials, Vienna, Austria.
| | - Sofia S Kantorovich
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.,Ural Federal University, Russian Federation/MMM Mathematics-Magnetism-Materials, Lenin Av. 51, Ekaterinburg 620000, Vienna, Austria
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11
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Weeber R, Kreissl P, Holm C. Magnetic field controlled behavior of magnetic gels studied using particle-based simulations. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2019-0106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Abstract
This contribution provides an overview of the study of soft magnetic materials using particle-based simulation models. We focus in particular on systems where thermal fluctuations are important. As a basis for further discussion, we first describe two-dimensional models which demonstrate two deformation mechanisms of magnetic gels in a homogeneous field. One is based on the change of magnetic interactions between magnetic particles as a response to an external field; the other is the result of magnetically blocked particles acting as cross-linkers. Based on the qualitative behavior directly observable in the two-dimensional models, we extend our description to three-dimensions. We begin with particle-cross-linked gels, as for those, our three-dimensional model also includes explicitly resolved polymer chains. Here, the polymer chains are represented by entropic springs, and the deformation of the gel is the result of the interaction between magnetic particles. We use this model to examine the influence of the magnetic spatial configuration of magnetic particles (uniaxial or isotropic) on the gel’s magnetomechanical behavior. A further part of the article will be dedicated to scale-bridging approaches such as systematic coarse-graining and models located at the boundary between particle-based and continuum modeling. We will conclude our article with a discussion of recent results for modeling time-dependent phenomena in magnetic-polymer composites. The discussion will be focused on a simulation model suitable for obtaining AC-susceptibility spectra for dilute ferrofluids including hydrodynamic interactions. This model will be the basis for studying the signature of particle–polymer coupling in magnetic hybrid materials. In the long run, we aim to compare material properties probed locally via the AC-susceptibility spectra to elastic moduli obtained for the system at a global level.
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Affiliation(s)
- Rudolf Weeber
- Institute for Computational Physics, University of Stuttgart , Stuttgart , Germany
| | - Patrick Kreissl
- Institute for Computational Physics, University of Stuttgart , Stuttgart , Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart , Stuttgart , Germany
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12
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Kuron M, Stewart C, de Graaf J, Holm C. An extensible lattice Boltzmann method for viscoelastic flows: complex and moving boundaries in Oldroyd-B fluids. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:1. [PMID: 33555445 PMCID: PMC7870644 DOI: 10.1140/epje/s10189-020-00005-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/14/2020] [Indexed: 05/26/2023]
Abstract
Most biological fluids are viscoelastic, meaning that they have elastic properties in addition to the dissipative properties found in Newtonian fluids. Computational models can help us understand viscoelastic flow, but are often limited in how they deal with complex flow geometries and suspended particles. Here, we present a lattice Boltzmann solver for Oldroyd-B fluids that can handle arbitrarily shaped fixed and moving boundary conditions, which makes it ideally suited for the simulation of confined colloidal suspensions. We validate our method using several standard rheological setups and additionally study a single sedimenting colloid, also finding good agreement with the literature. Our approach can readily be extended to constitutive equations other than Oldroyd-B. This flexibility and the handling of complex boundaries hold promise for the study of microswimmers in viscoelastic fluids.
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Affiliation(s)
- Michael Kuron
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569, Stuttgart, Germany.
| | - Cameron Stewart
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569, Stuttgart, Germany
| | - Joost de Graaf
- Institute for Theoretical Physics, Center for Extreme Matter and Emergent Phenomena, Utrecht University, Princetonplein 5, 3584 CC, Utrecht, The Netherlands
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569, Stuttgart, Germany
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13
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Kreissl P, Holm C, Weeber R. Frequency-dependent magnetic susceptibility of magnetic nanoparticles in a polymer solution: a simulation study. SOFT MATTER 2021; 17:174-183. [PMID: 33165470 DOI: 10.1039/d0sm01554g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Magnetic composite materials i.e. elastomers, polymer gels, or polymer solutions with embedded magnetic nanoparticles are useful for many technical and bio-medical applications. However, the microscopic details of the coupling mechanisms between the magnetic properties of the particles and the mechanical properties of the (visco)elastic polymer matrix remain unresolved. Here we study the response of a single-domain spherical magnetic nanoparticle that is suspended in a polymer solution to alternating magnetic fields. As interactions we consider only excluded volume interactions with the polymers and hydrodynamic interactions mediated through the solvent. The AC susceptibility spectra are calculated using a linear response Green-Kubo approach, and the influences of changing polymer concentration and polymer length are investigated. Our data is compared to recent measurements of the AC susceptibility for a typical magnetic composite system [Roeben et al., Colloid Polym. Sci., 2014, 2013-2023], and demonstrates the importance of hydrodynamic coupling in such systems.
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Affiliation(s)
- Patrick Kreissl
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
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14
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Kaiser M, Martinez Y, Schmidt AM, Sánchez PA, Kantorovich SS. Diffusion of single active-dipolar cubes in applied fields. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Carenza LN, Gonnella G, Lamura A, Negro G, Tiribocchi A. Lattice Boltzmann methods and active fluids. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:81. [PMID: 31250142 DOI: 10.1140/epje/i2019-11843-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/24/2019] [Indexed: 05/24/2023]
Abstract
We review the state of the art of active fluids with particular attention to hydrodynamic continuous models and to the use of Lattice Boltzmann Methods (LBM) in this field. We present the thermodynamics of active fluids, in terms of liquid crystals modelling adapted to describe large-scale organization of active systems, as well as other effective phenomenological models. We discuss how LBM can be implemented to solve the hydrodynamics of active matter, starting from the case of a simple fluid, for which we explicitly recover the continuous equations by means of Chapman-Enskog expansion. Going beyond this simple case, we summarize how LBM can be used to treat complex and active fluids. We then review recent developments concerning some relevant topics in active matter that have been studied by means of LBM: spontaneous flow, self-propelled droplets, active emulsions, rheology, active turbulence, and active colloids.
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Affiliation(s)
- Livio Nicola Carenza
- Dipartimento di Fisica, Università degli Studi di Bari, and INFN Sezione di Bari, Via Amendola 173, 70126, Bari, Italy
| | - Giuseppe Gonnella
- Dipartimento di Fisica, Università degli Studi di Bari, and INFN Sezione di Bari, Via Amendola 173, 70126, Bari, Italy.
| | - Antonio Lamura
- Istituto Applicazioni Calcolo, CNR, Via Amendola 122/D, 70126, Bari, Italy
| | - Giuseppe Negro
- Dipartimento di Fisica, Università degli Studi di Bari, and INFN Sezione di Bari, Via Amendola 173, 70126, Bari, Italy
| | - Adriano Tiribocchi
- Center for Life Nano Science@La Sapienza, Istituto Italiano di Tecnologia, 00161, Roma, Italy
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16
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Lee M, Szuttor K, Holm C. A computational model for bacterial run-and-tumble motion. J Chem Phys 2019; 150:174111. [PMID: 31067902 DOI: 10.1063/1.5085836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this article we present a computational model for the simulation of self-propelled anisotropic bacteria. To this end we use a self-propelled particle model and augment it with a statistical algorithm for the run-and-tumble motion. We derive an equation for the distribution of reorientations of the bacteria that we use to analyze the statistics of the random walk and that allows us to tune the behavior of our model to the characteristics of an E. coli bacterium. We validate our implementation in terms of a single swimmer and demonstrate that our model is capable of reproducing E. coli's run-and-tumble motion with excellent accuracy.
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Affiliation(s)
- Miru Lee
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Kai Szuttor
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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17
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Kuron M, Kreissl P, Holm C. Toward Understanding of Self-Electrophoretic Propulsion under Realistic Conditions: From Bulk Reactions to Confinement Effects. Acc Chem Res 2018; 51:2998-3005. [PMID: 30417644 DOI: 10.1021/acs.accounts.8b00285] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Active matter concerns itself with the study of particles that convert energy into work, typically motion of the particle itself. This field saw a surge of interest over the past decade, after the first micrometer-sized, man-made chemical motors were created. These particles served as a simple model system for studying in a well-controlled manner complex motion and cooperative behavior as known from biology. In addition, they have stimulated new efforts in understanding out-of-equilibrium statistical physics and started a revolution in microtechnology and robotics. Concentrated effort has gone into realizing these ambitions, and yet much remains unknown about the chemical motors themselves. The original designs for self-propelled particles relied on the conversion of the chemical energy of hydrogen peroxide into motion via catalytic decomposition taking place heterogeneously over the surface of the motor. This sets up gradients of chemical fields around the particle, which allow it to autophorese. That is, the interaction between the motor and the heterogeneously distributed solute species can drive fluid flow and the motor itself. There are two basic designs: the first relies on redox reactions taking place between the two sides of a bimetal, for example, a gold-platinum Janus sphere or nanorod. The second uses a catalytic layer of platinum inhomogeneously vapor-deposited onto a nonreactive particle. For convenience's sake, these can be referred to as redox motors and monometallic half-coated motors, respectively. To date, most researchers continue to rely on variations of these simple, yet elegant designs for their experiments. However, there is ongoing debate on the exact way chemical energy is transduced into motion in these motors. Many of the experimental observations on redox motors were successfully modeled via self-electrophoresis, while for half-coated motors there has been a strong focus on self-diffusiophoresis. Currently, there is mounting evidence that self-electrophoresis provides the dominant contribution to the observed speeds of half-coated motors, even if the vast majority of the reaction products are electroneutral. In this Account, we will summarize the most common electrophoretic propulsion model and discuss its strengths and weaknesses in relation to recent experiments. We will comment on the possible need to go beyond surface reactions and consider the entire medium as an "active fluid" that can create and annihilate charged species. This, together with confinement and collective effects, makes it difficult to gain a detailed understanding of these swimmers. The potentially dominant effect of confinement is highlighted on the basis of a recent study of an electro-osmotic pump that drives fluid along a substrate. Detailed analysis of this system allows for identification of the electro-osmotic driving mechanism, which is powered by micromolar salt concentrations. We will discuss how our latest numerical solver developments, based on the lattice Boltzmann method, should enable us to study collective behavior in systems comprised of these and other electrochemical motors in realistic environments. We conclude with an outlook on the future of modeling chemical motors that may facilitate the community's microtechnological ambitions.
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Affiliation(s)
- Michael Kuron
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Patrick Kreissl
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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18
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Dissipative Coupling of Fluid and Immersed Objects for Modelling of Cells in Flow. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2018; 2018:7842857. [PMID: 30363716 PMCID: PMC6180995 DOI: 10.1155/2018/7842857] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/18/2018] [Accepted: 09/03/2018] [Indexed: 11/29/2022]
Abstract
Modelling of cell flow for biomedical applications relies in many cases on the correct description of fluid-structure interaction between the cell membrane and the surrounding fluid. We analyse the coupling of the lattice-Boltzmann method for the fluid and the spring network model for the cells. We investigate the bare friction parameter of fluid-structure interaction that is mediated via dissipative coupling. Such coupling mimics the no-slip boundary condition at the interface between the fluid and object. It is an alternative method to the immersed boundary method. Here, the fluid-structure coupling is provided by forces penalising local differences between velocities of the object's boundaries and the surrounding fluid. The method includes a phenomenological friction coefficient that determines the strength of the coupling. This work aims at determination of proper values of such friction coefficient. We derive an explicit formula for computation of this coefficient depending on the mesh density assuming a reference friction is known. We validate this formula on spherical and ellipsoidal objects. We also provide sensitivity analysis of the formula on all parameters entering the model. We conclude that such formula may be used also for objects with irregular shapes provided that the triangular mesh covering the object's surface is in some sense uniform. Our findings are justified by two computational experiments where we simulate motion of a red blood cell in a capillary and in a shear flow. Both experiments confirm our results presented in this work.
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19
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Schwarzendahl FJ, Mazza MG. Maximum in density heterogeneities of active swimmers. SOFT MATTER 2018; 14:4666-4678. [PMID: 29717736 DOI: 10.1039/c7sm02301d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Suspensions of unicellular microswimmers such as flagellated bacteria or motile algae can exhibit spontaneous density heterogeneities at large enough concentrations. We introduce a novel model for biological microswimmers that creates the flow field of the corresponding microswimmers, and takes into account the shape anisotropy of the swimmer's body and stroke-averaged flagella. By employing multiparticle collision dynamics, we directly couple the swimmer's dynamics to the fluid's. We characterize the nonequilibrium phase diagram, as the filling fraction and Péclet number are varied, and find density heterogeneities in the distribution of both pullers and pushers, due to hydrodynamic instabilities. We find a maximum degree of clustering at intermediate filling fractions and at large Péclet numbers resulting from a competition of hydrodynamic and steric interactions between the swimmers. We develop an analytical theory that supports these results. This maximum might represent an optimum for the microorganisms' colonization of their environment.
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Affiliation(s)
- Fabian Jan Schwarzendahl
- Max-Planck-Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077 Göttingen, Germany.
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20
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Dubov AL, Molotilin TY, Vinogradova OI. Continuous electroosmotic sorting of particles in grooved microchannels. SOFT MATTER 2017; 13:7498-7504. [PMID: 28936528 DOI: 10.1039/c7sm00986k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We propose a novel microfluidic fractionation concept suitable for neutrally buoyant micron-sized particles. This approach takes advantage of the ability of grooved channel walls oriented at an angle to the direction of an external electric field to generate a transverse electroosmotic flow. Using computer simulations, we first demonstrate that the velocity of this secondary transverse flow depends on the distance from the wall, so neutrally buoyant particles, depending on their size and initial location, will experience different lateral displacements. We then optimize the geometry and orientation of the surface texture of the channel walls to maximize the efficiency of particle fractionation. Our method is illustrated in a full scale computer experiment where we mimic the typical microchannel with a bottom grooved wall and a source of polydisperse particles that are carried along the channel by the forward electroosmotic flow. Our simulations show that the particle dispersion can be efficiently separated by size even in a channel that is only a few texture periods long. These results can guide the design of novel microfluidic devices for efficient sorting of microparticles.
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Affiliation(s)
- Alexander L Dubov
- A.N.Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31 Leninsky Prospect, 119071 Moscow, Russia.
| | - Taras Y Molotilin
- A.N.Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31 Leninsky Prospect, 119071 Moscow, Russia.
| | - Olga I Vinogradova
- A.N.Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31 Leninsky Prospect, 119071 Moscow, Russia. and Department of Physics, M.V.Lomonosov Moscow State University, 119991 Moscow, Russia and DWI - Leibniz Institute for Interactive Materials, RWTH Aachen, Forckenbeckstr. 50, 52056 Aachen, Germany
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21
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Kabedev A, Ross-Lonergan M, Lobaskin V. Hydrodynamic lift forces on solutes in a tilted nanopillar array: A computer simulation study. Electrophoresis 2017; 38:2479-2487. [PMID: 28755416 DOI: 10.1002/elps.201700130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/04/2017] [Accepted: 07/17/2017] [Indexed: 11/10/2022]
Abstract
We study solute transport in a microfluidic channel, where the walls hold an array of tilted rigid nanopillars. By solving numerically the flow equations in the channel, we show that a combination of hydrodynamic effects with excluded volume interactions between the solute particles and the pillars leads to a hydrodynamic lift effect, which varies with the particle size, and depends in a strongly nonlinear fashion on the flow rate. We show that the lift force can be sufficiently strong to drive the solute accumulation or removal from the pillar region and can be switched to the opposite direction by variation of the shear rate or driving pressure. We also demonstrate that the nanopillar array can be used to selectively attract particles of certain size and enhance solute trapping at the surface.
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Affiliation(s)
- Aleksei Kabedev
- School of Physics, University College Dublin, Dublin 4, Ireland
| | - Mark Ross-Lonergan
- Nevis Laboratories, Department of Physics, Columbia University, Irvington, NY, USA
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22
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Rau T, Weik F, Holm C. A dsDNA model optimized for electrokinetic applications. SOFT MATTER 2017; 13:3918-3926. [PMID: 28497827 DOI: 10.1039/c7sm00270j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a coarse-grained (CG) model of a charged double-stranded DNA immersed in an electrolyte solution that can be used for a variety of electrokinetic applications. The model is based on an earlier rigid and immobile model of Weik et al. and includes now semi-flexibility and mobility, so that DNA dynamics can be sufficiently captured to simulate a full nanopore translocation process. To this end we couple the DNA hydrodynamically via a raspberry approach to a lattice-Boltzmann fluid and parametrize the counterions with a distant dependent friction. The electrokinetic properties of the CG DNA model inside an infinite cylinder is fitted against experimental data from Smeets et al. and all-atom simulation data from Kesselheim et al. The stiffness of our CG DNA is modeled via a harmonic angle potential fitted against experimental data of Brunet et al. Finally, the quality of our tuned parameters is tested by measuring the electrophoretic mobility of our DNA model for various numbers of base pairs and salt concentrations. Our results compare excellently with the experimental data sets of Stellwagen et al. and Hoagland et al.
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Affiliation(s)
- Tobias Rau
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, Stuttgart, Germany
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23
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de Graaf J, Stenhammar J. Lattice-Boltzmann simulations of microswimmer-tracer interactions. Phys Rev E 2017; 95:023302. [PMID: 28297968 DOI: 10.1103/physreve.95.023302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Indexed: 06/06/2023]
Abstract
Hydrodynamic interactions in systems composed of self-propelled particles, such as swimming microorganisms and passive tracers, have a significant impact on the tracer dynamics compared to the equivalent "dry" sample. However, such interactions are often difficult to take into account in simulations due to their computational cost. Here, we perform a systematic investigation of swimmer-tracer interaction using an efficient force-counterforce-based lattice-Boltzmann (LB) algorithm [De Graaf et al., J. Chem. Phys. 144, 134106 (2016)JCPSA60021-960610.1063/1.4944962] in order to validate its ability to capture the relevant low-Reynolds-number physics. We show that the LB algorithm reproduces far-field theoretical results well, both in a system with periodic boundary conditions and in a spherical cavity with no-slip walls, for which we derive expressions here. The force-lattice coupling of the LB algorithm leads to a "smearing out" of the flow field, which strongly perturbs the tracer trajectories at close swimmer-tracer separations, and we analyze how this effect can be accurately captured using a simple renormalized hydrodynamic theory. Finally, we show that care must be taken when using LB algorithms to simulate systems of self-propelled particles, since its finite momentum transport time can lead to significant deviations from theoretical predictions based on Stokes flow. These insights should prove relevant to the future study of large-scale microswimmer suspensions using these methods.
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Affiliation(s)
- Joost de Graaf
- SUPA, School of Physics and Astronomy, University of Edinburgh, King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, United Kingdom
| | - Joakim Stenhammar
- Division of Physical Chemistry, Lund University, Box 124, S-221 00 Lund, Sweden
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24
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Molotilin TY, Lobaskin V, Vinogradova OI. Electrophoresis of Janus particles: A molecular dynamics simulation study. J Chem Phys 2016; 145:244704. [DOI: 10.1063/1.4972522] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Taras Y. Molotilin
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31 Leninsky Prospect, 119071 Moscow, Russia
| | - Vladimir Lobaskin
- School of Physics and Complex and Adaptive Systems Lab, University College Dublin, Belfield, Dublin 4, Ireland
| | - Olga I. Vinogradova
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31 Leninsky Prospect, 119071 Moscow, Russia
- Department of Physics, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia
- DWI - Leibniz Institute for Interactive Materials, RWTH Aachen, Forckenbeckstraße 50, 52056 Aachen, Germany
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25
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Kuron M, Rempfer G, Schornbaum F, Bauer M, Godenschwager C, Holm C, de Graaf J. Moving charged particles in lattice Boltzmann-based electrokinetics. J Chem Phys 2016; 145:214102. [DOI: 10.1063/1.4968596] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michael Kuron
- Institut für Computerphysik, Universität Stuttgart, 70550 Stuttgart, Germany
| | - Georg Rempfer
- Institut für Computerphysik, Universität Stuttgart, 70550 Stuttgart, Germany
| | - Florian Schornbaum
- Lehrstuhl für Systemsimulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Martin Bauer
- Lehrstuhl für Systemsimulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Christian Godenschwager
- Lehrstuhl für Systemsimulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Christian Holm
- Institut für Computerphysik, Universität Stuttgart, 70550 Stuttgart, Germany
| | - Joost de Graaf
- Institut für Computerphysik, Universität Stuttgart, 70550 Stuttgart, Germany
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26
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Ilse SE, Holm C, de Graaf J. Surface roughness stabilizes the clustering of self-propelled triangles. J Chem Phys 2016; 145:134904. [PMID: 27782450 DOI: 10.1063/1.4963804] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sven Erik Ilse
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Joost de Graaf
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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27
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Rempfer G, Davies GB, Holm C, de Graaf J. Reducing spurious flow in simulations of electrokinetic phenomena. J Chem Phys 2016; 145:044901. [DOI: 10.1063/1.4958950] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Georg Rempfer
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Gary B. Davies
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Joost de Graaf
- School of Physics and Astronomy, University of Edinburgh, Scotland, Edinburgh EH9 3JL, United Kingdom
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28
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de Graaf J, Mathijssen AJTM, Fabritius M, Menke H, Holm C, Shendruk TN. Understanding the onset of oscillatory swimming in microchannels. SOFT MATTER 2016; 12:4704-4708. [PMID: 27184912 DOI: 10.1039/c6sm00939e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Self-propelled colloids (swimmers) in confining geometries follow trajectories determined by hydrodynamic interactions with the bounding surfaces. However, typically these interactions are ignored or truncated to the lowest order. We demonstrate that higher-order hydrodynamic moments cause rod-like swimmers to follow oscillatory trajectories in quiescent fluid between two parallel plates, using a combination of lattice-Boltzmann simulations and far-field calculations. This behavior occurs even far from the confining walls and does not require lubrication results. We show that a swimmer's hydrodynamic quadrupole moment is crucial to the onset of the oscillatory trajectories. This insight allows us to develop a simple model for the dynamics near the channel center based on these higher hydrodynamic moments, and suggests opportunities for trajectory-based experimental characterization of swimmers' hydrodynamic properties.
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Affiliation(s)
- Joost de Graaf
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
| | | | - Marc Fabritius
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
| | - Henri Menke
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany.
| | - Tyler N Shendruk
- The Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford, OX1 3NP, UK
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29
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Hoell C, Löwen H. Colloidal suspensions of C-particles: Entanglement, percolation and microrheology. J Chem Phys 2016; 144:174901. [DOI: 10.1063/1.4947237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Christian Hoell
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
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30
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de Graaf J, Menke H, Mathijssen AJTM, Fabritius M, Holm C, Shendruk TN. Lattice-Boltzmann hydrodynamics of anisotropic active matter. J Chem Phys 2016; 144:134106. [DOI: 10.1063/1.4944962] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Joost de Graaf
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Henri Menke
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | | | - Marc Fabritius
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Tyler N. Shendruk
- The Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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31
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de Graaf J, Peter T, Fischer LP, Holm C. The Raspberry model for hydrodynamic interactions revisited. II. The effect of confinement. J Chem Phys 2015; 143:084108. [PMID: 26328819 DOI: 10.1063/1.4928503] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The so-called "raspberry" model refers to the hybrid lattice-Boltzmann (LB) and Langevin molecular dynamics schemes for simulating the dynamics of suspensions of colloidal particles, originally developed by Lobaskin and Dünweg [New J. Phys. 6, 54 (2004)], wherein discrete surface points are used to achieve fluid-particle coupling. In this paper, we present a follow up to our study of the effectiveness of the raspberry model in reproducing hydrodynamic interactions in the Stokes regime for spheres arranged in a simple-cubic crystal [Fischer et al., J. Chem. Phys. 143, 084107 (2015)]. Here, we consider the accuracy with which the raspberry model is able to reproduce such interactions for particles confined between two parallel plates. To this end, we compare our LB simulation results to established theoretical expressions and finite-element calculations. We show that there is a discrepancy between the translational and rotational mobilities when only surface coupling points are used, as also found in Part I of our joint publication. We demonstrate that adding internal coupling points to the raspberry can be used to correct said discrepancy in confining geometries as well. Finally, we show that the raspberry model accurately reproduces hydrodynamic interactions between a spherical colloid and planar walls up to roughly one LB lattice spacing.
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Affiliation(s)
- Joost de Graaf
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Toni Peter
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Lukas P Fischer
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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