| 1. |
- Angelescu, Daniel, et al.
(author)
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Packaging of a flexible polyelectrolyte inside a viral capsid: Effect of salt concentration and salt valence
- 2007
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In: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 111:29, s. 8477-8485
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Journal article (peer-reviewed)abstract
- The effect of salt on the location and structure of a flexible polyelectrolyte confined inside a viral capsid and the Donnan equilibrium of the salt across the capsid have been examined using a coarse-grained model solved by Monte Carlo simulations. The polyelectrolyte was represented by a linear jointed chain of charged beads, and the capsid was represented by a spherical shell with embedded charges. At low salt concentration, the polyelectrolyte was strongly adsorbed onto the inner capsid surface, whereas at high salt concentration it was located preferentially in the central part of the capsid. Under the condition of equal Debye screening length, the electrostatic screening increased as the valence of the polyelectrolyte counterion was increased. The distribution of the small cations and anions was unequal across the capsid. An excess of polyelectrolyte counterions occurred inside the capsid, and the excess increased with the salt concentration. A simplified representation of the small ions through the use of the screened Coulomb potential provided only a qualitatively correct picture; the electrostatic screening originating from the small ions was exaggerated.
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| 2. |
- Aporvari, M. S., et al.
(author)
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Anisotropic dynamics of a self-assembled colloidal chain in an active bath
- 2020
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In: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-683X .- 1744-6848. ; 16:24, s. 5609-5614
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Journal article (peer-reviewed)abstract
- Anisotropic macromolecules exposed to non-equilibrium (active) noise are very common in biological systems, and an accurate understanding of their anisotropic dynamics is therefore crucial. Here, we experimentally investigate the dynamics of isolated chains assembled from magnetic microparticles at a liquid-air interface and moving in an active bath consisting of motile E. coli bacteria. We investigate both the internal chain dynamics and the anisotropic center-of-mass dynamics through particle tracking. We find that both the internal and center-of-mass dynamics are greatly enhanced compared to the passive case, i.e., a system without bacteria, and that the center-of-mass diffusion coefficient D features a non- monotonic dependence as a function of the chain length. Furthermore, our results show that the relationship between the components of D parallel and perpendicular with respect to the direction of the applied magnetic field is preserved in the active bath compared to the passive case, with a higher diffusion in the parallel direction, in contrast to previous findings in the literature. We argue that this qualitative difference is due to subtle differences in the experimental geometry and conditions and the relative roles played by long-range hydrodynamic interactions and short-range collisions.
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| 3. |
- Azari, Arash, et al.
(author)
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Directed Self-Assembly of Polarizable Ellipsoids in an External Electric Field
- 2017
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In: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 33:48, s. 13834-13840
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Journal article (peer-reviewed)abstract
- The interplay between shape anisotropy and directed long-range interactions enables the self-assembly of complex colloidal structures. As a recent highlight, ellipsoidal particles polarized in an external electric field were observed to associate into well-defined tubular structures. In this study, we systematically investigate such directed self-assembly using Monte Carlo simulations of a two-point-charge model of polarizable prolate ellipsoids. In spite of its simplicity and computational efficiency, we demonstrate that the model is capable of capturing the complex structures observed in experiments on ellipsoidal colloids at low volume fractions. We show that, at sufficiently high electric field strength, the anisotropy in shape and electrostatic interactions causes a transition from three-dimensional crystal structures observed at low aspect ratios to two-dimensional sheets and tubes at higher aspect ratios. Our work thus illustrates the rich self-assembly behavior accessible when exploiting the interplay between competing long- and short-range anisotropic interactions in colloidal systems.
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| 4. |
- Bárdfalvy, Dóra, et al.
(author)
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Collective motion in a sheet of microswimmers
- 2024
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In: Communications Physics. - 2399-3650. ; 7:1
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Journal article (peer-reviewed)abstract
- Self-propelled particles such as bacteria or algae swimming through a fluid are non-equilibrium systems where particle motility breaks microscopic detailed balance, often resulting in large-scale collective motion. Previous theoretical work has identified long-ranged hydrodynamic interactions as the driver of collective motion in unbounded suspensions of rear-actuated (“pusher”) microswimmers. In contrast, most experimental studies of collective motion in microswimmer suspensions have been carried out in restricted geometries where both the swimmers’ motion and their long-range flow fields become altered due to the proximity of a boundary. Here, we study numerically a minimal model of microswimmers in such a restricted geometry, where the particles move in the midplane between two no-slip walls. For pushers, we demonstrate collective motion with short-ranged order, in contrast with the long-ranged flows observed in unbounded systems. For front-actuated (“puller”) microswimmers, we discover a long-wavelength density instability resulting in the formation of dense microswimmer clusters. Both types of collective motion are fundamentally different from their previously studied counterparts in unbounded domains. Our results show that this difference is dictated by the geometrical restriction of the swimmers’ motion, while hydrodynamic screening due to the presence of a wall is subdominant in determining the suspension’s collective state.
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| 5. |
- Bárdfalvy, Dóra, et al.
(author)
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Particle-resolved lattice Boltzmann simulations of 3-dimensional active turbulence
- 2019
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In: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-6848 .- 1744-683X. ; 15:39, s. 7747-7756
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Journal article (peer-reviewed)abstract
- Collective behaviour in suspensions of microswimmers is often dominated by the impact of long-ranged hydrodynamic interactions. These phenomena include active turbulence, where suspensions of pusher bacteria at sufficient densities exhibit large-scale, chaotic flows. To study this collective phenomenon, we use large-scale (up to N = 3 × 106) particle-resolved lattice Boltzmann simulations of model microswimmers described by extended stresslets. Such system sizes enable us to obtain quantitative information about both the transition to active turbulence and characteristic features of the turbulent state itself. In the dilute limit, we test analytical predictions for a number of static and dynamic properties against our simulation results. For higher swimmer densities, where swimmer-swimmer interactions become significant, we numerically show that the length- and timescales of the turbulent flows increase steeply near the predicted finite-system transition density.
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| 6. |
- Bárdfalvy, Dóra, et al.
(author)
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Symmetric Mixtures of Pusher and Puller Microswimmers Behave as Noninteracting Suspensions
- 2020
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In: Physical Review Letters. - 0031-9007. ; 125:1
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Journal article (peer-reviewed)abstract
- Suspensions of rear- and front-actuated microswimmers immersed in a fluid, known respectively as "pushers"and "pullers,"display qualitatively different collective behaviors: beyond a characteristic density, pusher suspensions exhibit a hydrodynamic instability leading to collective motion known as active turbulence, a phenomenon which is absent for pullers. In this Letter, we describe the collective dynamics of a binary pusher-puller mixture using kinetic theory and large-scale particle-resolved simulations. We derive and verify an instability criterion, showing that the critical density for active turbulence moves to higher values as the fraction χ of pullers is increased and disappears for χ≥0.5. We then show analytically and numerically that the two-point hydrodynamic correlations of the 1:1 mixture are equal to those of a suspension of noninteracting swimmers. Strikingly, our numerical analysis furthermore shows that the full probability distribution of the fluid velocity fluctuations collapses onto the one of a noninteracting system at the same density, where swimmer-swimmer correlations are strictly absent. Our results thus indicate that the fluid velocity fluctuations in 1:1 pusher-puller mixtures are exactly equal to those of the corresponding noninteracting suspension at any density, a surprising cancellation with no counterpart in equilibrium long-range interacting systems.
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| 7. |
- Bergman, Maxime J., et al.
(author)
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On the role of softness in ionic microgel interactions
- 2021
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In: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-683X .- 1744-6848. ; 17:44, s. 10063-10072
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Journal article (peer-reviewed)abstract
- Thermoresponsive microgels are a popular model system to study phase transitions in soft matter, because temperature directly controls their volume fraction. Ionic microgels are additionally pH-responsive and possess a rich phase diagram. Although effective interaction potentials between microgel particles have been proposed, these have never been fully tested, leading to a gap in our understanding of the link between single-particle and collective properties. To help resolve this gap, four sets of ionic microgels with varying crosslinker density were synthesised and characterised using light scattering techniques and confocal microscopy. The resultant structural and dynamical information was used to investigate how particle softness affects the phase behaviour of ionic microgels and to validate the proposed interaction potential. We find that the architecture of the microgel plays a marked role in its phase behaviour. Rather than the ionic charges, it is the dangling ends which drive phase transitions and interactions at low concentration. Comparison to theory underlines the need for a refined theoretical model which takes into consideration these close-contact interactions. This journal is
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| 8. |
- Bröker, Stephan, et al.
(author)
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Pair-distribution function of active Brownian spheres in three spatial dimensions : simulation results and analytical representation
- 2023
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In: Soft Matter. - 1744-683X. ; 20:1, s. 224-244
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Journal article (peer-reviewed)abstract
- The pair-distribution function, which provides information about correlations in a system of interacting particles, is one of the key objects of theoretical soft matter physics. In particular, it allows for microscopic insights into the phase behavior of active particles. While this function is by now well studied for two-dimensional active matter systems, the more complex and more realistic case of three-dimensional systems is not well understood by now. In this work, we analyze the full pair-distribution function of spherical active Brownian particles interacting via a Weeks-Chandler-Andersen potential in three spatial dimensions using Brownian dynamics simulations. Besides extracting the structure of the pair-distribution function from the simulations, we obtain an analytical representation for this function, parametrized by activity and concentration, which takes into account the symmetries of a homogeneous stationary state. Our results are useful as input to quantitative models of active Brownian particles and advance our understanding of the microstructure in dense active fluids.
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| 9. |
- de Graaf, Joost, et al.
(author)
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Lattice-Boltzmann simulations of microswimmer-tracer interactions
- 2017
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In: Physical Review E: covering statistical, nonlinear, biological, and soft matter physics. - 2470-0045. ; 95:2
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Journal article (peer-reviewed)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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| 10. |
- de Graaf, Joost, et al.
(author)
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Stirring by periodic arrays of microswimmers
- 2017
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In: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 811, s. 487-498
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Journal article (peer-reviewed)abstract
- The interaction between swimming micro-organisms or artificial self-propelled colloids and passive (tracer) particles in a fluid leads to enhanced diffusion of the tracers. This enhancement has attracted strong interest, as it could lead to new strategies to tackle the difficult problem of mixing on a microfluidic scale. Most of the theoretical work on this topic has focused on hydrodynamic interactions between the tracers and swimmers in a bulk fluid. However, in simulations, periodic boundary conditions (PBCs) are often imposed on the sample and the fluid. Here, we theoretically analyse the effect of PBCs on the hydrodynamic interactions between tracer particles and microswimmers. We formulate an Ewald sum for the leading-order stresslet singularity produced by a swimmer to probe the effect of PBCs on tracer trajectories. We find that introducing periodicity into the system has a surprisingly significant effect, even for relatively small swimmer–tracer separations. We also find that the bulk limit is only reached for very large system sizes, which are challenging to simulate with most hydrodynamic solvers.
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