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Negro G, Caporusso CB, Digregorio P, Gonnella G, Lamura A, Suma A. Hydrodynamic effects on the liquid-hexatic transition of active colloids. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2022; 45:75. [PMID: 36098879 PMCID: PMC9470657 DOI: 10.1140/epje/s10189-022-00230-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 08/25/2022] [Indexed: 05/06/2023]
Abstract
We study numerically the role of hydrodynamics in the liquid-hexatic transition of active colloids at intermediate activity, where motility induced phase separation (MIPS) does not occur. We show that in the case of active Brownian particles (ABP), the critical density of the transition decreases upon increasing the particle's mass, enhancing ordering, while self-propulsion has the opposite effect in the activity regime considered. Active hydrodynamic particles (AHP), instead, undergo the liquid-hexatic transition at higher values of packing fraction [Formula: see text] than the corresponding ABP, suggesting that hydrodynamics have the net effect of disordering the system. At increasing densities, close to the hexatic-liquid transition, we found in the case of AHP the appearance of self-sustained organized motion with clusters of particles moving coherently.
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Affiliation(s)
- G Negro
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, 70126, Italy
| | - C B Caporusso
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, 70126, Italy.
| | - P Digregorio
- Centre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Batochimie, Avenue Forel 2, 1015, Lausanne, Switzerland
| | - G Gonnella
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, 70126, Italy
| | - A Lamura
- Istituto Applicazioni Calcolo, CNR, Via Amendola 122/D, 70126, Bari, Italy
| | - A Suma
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, Bari, 70126, Italy
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Haxton TK, Hedges LO, Whitelam S. Crystallization and arrest mechanisms of model colloids. SOFT MATTER 2015; 11:9307-9320. [PMID: 26428696 DOI: 10.1039/c5sm01833a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We performed dynamic simulations of spheres with short-range attractive interactions for many values of interaction strength and range. Fast crystallization occurs in a localized region of this parameter space, but the character of crystallization pathways is not uniform within this region. Pathways range from one-step, in which a crystal nucleates directly from a gas, to two-step, in which substantial liquid-like clusters form and only subsequently become crystalline. Crystallization can fail because of slow nucleation from either gas or liquid, or because of dynamic arrest caused by strong interactions. Arrested states are characterized by the formation of networks of face-sharing tetrahedra that can be detected by a local common neighbor analysis.
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Affiliation(s)
- Thomas K Haxton
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Lester O Hedges
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. and Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Fischer LP, Peter T, Holm C, de Graaf J. The raspberry model for hydrodynamic interactions revisited. I. Periodic arrays of spheres and dumbbells. J Chem Phys 2015; 143:084107. [PMID: 26328818 DOI: 10.1063/1.4928502] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The so-called "raspberry" model refers to the hybrid lattice-Boltzmann and Langevin molecular dynamics scheme 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. This technique has been used in many simulation studies on the behavior of colloids. However, there are fundamental questions with regards to the use of this model. In this paper, we examine the accuracy with which the raspberry method is able to reproduce Stokes-level hydrodynamic interactions when compared to analytic expressions for solid spheres in simple-cubic crystals. To this end, we consider the quality of numerical experiments that are traditionally used to establish these properties and we discuss their shortcomings. We show that there is a discrepancy between the translational and rotational mobility reproduced by the simple raspberry model and present a way to numerically remedy this problem by adding internal coupling points. Finally, we examine a non-convex shape, namely, a colloidal dumbbell, and show that the filled raspberry model replicates the desired hydrodynamic behavior in bulk for this more complicated shape. Our investigation is continued in de Graaf et al. [J. Chem. Phys. 143, 084108 (2015)], wherein we consider the raspberry model in the confining geometry of two parallel plates.
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Affiliation(s)
- Lukas P Fischer
- 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
| | - Christian Holm
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Joost de Graaf
- Institute for Computational Physics (ICP), University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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Affiliation(s)
- Jimaan Sané
- Rudolf Peierls Centre for Theoretical Physics , Oxford, United Kingdom
- Department of Chemistry, Cambridge University , Cambridge, United Kingdom
| | - Johan T. Padding
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology , Eindhoven, The Netherlands
| | - Ard A. Louis
- Rudolf Peierls Centre for Theoretical Physics , Oxford, United Kingdom
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Dorfman KD, Gupta D, Jain A, Muralidhar A, Tree DR. Hydrodynamics of DNA confined in nanoslits and nanochannels. THE EUROPEAN PHYSICAL JOURNAL. SPECIAL TOPICS 2014; 223:3179-3200. [PMID: 25566349 PMCID: PMC4282777 DOI: 10.1140/epjst/e2014-02326-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Modeling the dynamics of a confined, semi exible polymer is a challenging problem, owing to the complicated interplay between the configurations of the chain, which are strongly affected by the length scale for the confinement relative to the persistence length of the chain, and the polymer-wall hydrodynamic interactions. At the same time, understanding these dynamics are crucial to the advancement of emerging genomic technologies that use confinement to stretch out DNA and "read" a genomic signature. In this mini-review, we begin by considering what is known experimentally and theoretically about the friction of a wormlike chain such as DNA confined in a slit or a channel. We then discuss how to estimate the friction coefficient of such a chain, either with dynamic simulations or via Monte Carlo sampling and the Kirk-wood pre-averaging approximation. We then review our recent work on computing the diffusivity of DNA in nanoslits and nanochannels, and conclude with some promising avenues for future work and caveats about our approach.
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Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Aashish Jain
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
- Materials Research Laboratory, University of California – Santa Barbara, Santa Barbara, CA 93106 USA
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Three dimensional simulation dynamics for the dilute colloidal suspensions of rod-like polymer particles flowing in the bulk and near solid boundaries. Macromol Res 2013. [DOI: 10.1007/s13233-013-1158-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Batôt G, Dahirel V, Mériguet G, Louis AA, Jardat M. Dynamics of solutes with hydrodynamic interactions: comparison between Brownian dynamics and stochastic rotation dynamics simulations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:043304. [PMID: 24229301 DOI: 10.1103/physreve.88.043304] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Indexed: 06/02/2023]
Abstract
The dynamics of particles in solution or suspension is influenced by thermal fluctuations and hydrodynamic interactions. Several mesoscale methods exist to account for these solvent-induced effects such as Brownian dynamics with hydrodynamic interactions and hybrid molecular dynamics-stochastic rotation dynamics methods. Here we compare two ways of coupling solutes to the solvent with stochastic rotation dynamics (SRD) to Brownian dynamics with and without explicit hydrodynamic interactions. In the first SRD scheme [SRD with collisional coupling (CC)] the solutes participate in the collisional step with the solvent and in the second scheme [SRD with central force coupling (CFC)] the solutes interact through direct forces with the solvent, generating slip boundary conditions. We compare the transport coefficients of neutral and charged solutes in a model system obtained by these simulation schemes. Brownian dynamics without hydrodynamic interactions is used as a reference to quantify the influence of hydrodynamics on the transport coefficients as modeled by the different methods. We show that, in the dilute range, the SRD CFC method provides results similar to those of Brownian dynamics with hydrodynamic interactions for the diffusion coefficients and for the electrical conductivity. The SRD CC scheme predicts diffusion coefficients close to those obtained by Brownian dynamic simulations without hydrodynamic interactions, but accounts for part of the influence of hydrodynamics on the electrical conductivity.
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Affiliation(s)
- G Batôt
- UPMC Univ Paris 06, UMR CNRS 7195 PECSA, F-75005 Paris, France
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Three-dimensional simulations for the dynamics of dilute colloidal suspensions of ellipsoidal-like particles flowing in the bulk and near solid boundaries. POLYMER 2013. [DOI: 10.1016/j.polymer.2013.01.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Lüsebrink D, Yang M, Ripoll M. Thermophoresis of colloids by mesoscale simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:284132. [PMID: 22739145 DOI: 10.1088/0953-8984/24/28/284132] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The motion of a colloid induced by a temperature gradient is simulated by means of multiparticle collision dynamics, a mesoscale simulation technique. Two algorithms to quantify the thermophoretic behavior are employed and contrasted. The validity of the methods is verified as a function of the temperature gradient, system size, and algorithm parameters. The variation of the solvent-colloid interaction from attractive to purely repulsive interestingly results in the change of the colloid behavior from thermophobic to thermophilic.
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Affiliation(s)
- Daniel Lüsebrink
- Theoretical Soft-Matter and Biophysics, Institute of Complex Systems, Forschungszentrum Jülich, 52425 Jülich, Germany
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Götze IO, Gompper G. Dynamic self-assembly and directed flow of rotating colloids in microchannels. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:031404. [PMID: 22060368 DOI: 10.1103/physreve.84.031404] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Indexed: 05/23/2023]
Abstract
Nonequilibrium structure formation and dynamics in suspensions of superparamagnetic colloids driven by an external rotating magnetic field are studied by particle-based mesoscale hydrodynamics simulations in confined geometry. We address the fundamental question how the rotation of the colloids about their own axes can be converted into a translational motion by breaking the symmetry of the confining geometry. We study a two-dimensional system of colloids with short-range repulsive interactions, which mimics flow in shallow microchannels. In straight channels, we observe a two-way traffic but--for symmetry reasons--no net transport. However, by keeping some colloids fixed near one of the two walls, net transport can be achieved. This approach allows the control and switchability of the flow in complex microchannel networks. A minimal geometry that fulfills the requirement of broken symmetry are ring channels. We determine the translational velocity of the spinning colloids and study its dependence on the channel width for various median radii. We conclude that spinning colloids present a promising alternative for flow generation and control in microfluidic devices.
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Affiliation(s)
- Ingo O Götze
- Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich D-52425, Germany.
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Sané J, Padding JT, Louis AA. The crossover from single file to Fickian diffusion. Faraday Discuss 2010; 144:285-99; discussion 323-45, 467-81. [DOI: 10.1039/b905378f] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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