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  1. Semiflexible slender filaments are ubiquitous in nature and cell biology, including in the cytoskeleton, where reorganization of actin filaments allows the cell to move and divide. Most methods for simulating semiflexible inextensible fibers/polymers are based on discrete (bead-link or blob-link) models, which become prohibitively expensive in the slender limit when hydrodynamics is accounted for. In this paper, we develop a novel coarse-grained approach for simulating fluctuating slender filaments with hydrodynamic interactions. Our approach is tailored to relatively stiff fibers whose persistence length is comparable to or larger than their length and is based on three major contributions. First, we discretize the filament centerline using a coarse non-uniform Chebyshev grid, on which we formulate a discrete constrained Gibbs–Boltzmann (GB) equilibrium distribution and overdamped Langevin equation for the evolution of unit-length tangent vectors. Second, we define the hydrodynamic mobility at each point on the filament as an integral of the Rotne–Prager–Yamakawa kernel along the centerline and apply a spectrally accurate “slender-body” quadrature to accurately resolve the hydrodynamics. Third, we propose a novel midpoint temporal integrator, which can correctly capture the Ito drift terms that arise in the overdamped Langevin equation. For two separate examples, we verify that the equilibrium distribution for the Chebyshev grid is a good approximation of the blob-link one and that our temporal integrator for overdamped Langevin dynamics samples the equilibrium GB distribution for sufficiently small time step sizes. We also study the dynamics of relaxation of an initially straight filament and find that as few as 12 Chebyshev nodes provide a good approximation to the dynamics while allowing a time step size two orders of magnitude larger than a resolved blob-link simulation. We conclude by applying our approach to a suspension of cross-linked semiflexible fibers (neglecting hydrodynamic interactions between fibers), where we study how semiflexible fluctuations affect bundling dynamics. We find that semiflexible filaments bundle faster than rigid filaments even when the persistence length is large, but show that semiflexible bending fluctuations only further accelerate agglomeration when the persistence length and fiber length are of the same order. 
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  2. Soft microbots based on magnetic Pickering emulsions exhibit tractions higher than their rigid counterparts. 
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  3. We develop a linearly scaling variant of the force coupling method [K. Yeo and M. R. Maxey, J. Fluid Mech. 649, 205–231 (2010)] for computing hydrodynamic interactions among particles confined to a doubly periodic geometry with either a single bottom wall or two walls (slit channel) in the aperiodic direction. Our spectrally accurate Stokes solver uses the fast Fourier transform in the periodic xy plane and Chebyshev polynomials in the aperiodic z direction normal to the wall(s). We decompose the problem into two problems. The first is a doubly periodic subproblem in the presence of particles (source terms) with free-space boundary conditions in the z direction, which we solve by borrowing ideas from a recent method for rapid evaluation of electrostatic interactions in doubly periodic geometries [Maxian et al., J. Chem. Phys. 154, 204107 (2021)]. The second is a correction subproblem to impose the boundary conditions on the wall(s). Instead of the traditional Gaussian kernel, we use the exponential of a semicircle kernel to model the source terms (body force) due to the presence of particles and provide optimum values for the kernel parameters that ensure a given hydrodynamic radius with at least two digits of accuracy and rotational and translational invariance. The computation time of our solver, which is implemented in graphical processing units, scales linearly with the number of particles, and allows computations with about a million particles in less than a second for a sedimented layer of colloidal microrollers. We find that in a slit channel, a driven dense suspension of microrollers maintains the same two-layer structure as above a single wall, but moves at a substantially lower collective speed due to increased confinement. 
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    We perform detailed computational and experimental measurements of the driven dynamics of a dense, uniform suspension of sedimented microrollers driven by a magnetic field rotating around an axis parallel to the floor. We develop a lubrication-corrected Brownian dynamics method for dense suspensions of driven colloids sedimented above a bottom wall. The numerical method adds lubrication friction between nearby pairs of particles, as well as particles and the bottom wall, to a minimally-resolved model of the far-field hydrodynamic interactions. Our experiments combine fluorescent labeling with particle tracking to trace the trajectories of individual particles in a dense suspension, and to measure their propulsion velocities. Previous computational studies [B. Sprinkle et al. , J. Chem. Phys. , 2017, 147 , 244103] predicted that at sufficiently high densities a uniform suspension of microrollers separates into two layers, a slow monolayer right above the wall, and a fast layer on top of the bottom layer. Here we verify this prediction, showing good quantitative agreement between the bimodal distribution of particle velocities predicted by the lubrication-corrected Brownian dynamics and those measured in the experiments. The computational method accurately predicts the rate at which particles are observed to switch between the slow and fast layers in the experiments. We also use our numerical method to demonstrate the important role that pairwise lubrication plays in motility-induced phase separation in dense monolayers of colloidal microrollers, as recently suggested for suspensions of Quincke rollers [D. Geyer et al. , Phys. Rev. X , 2019, 9 (3), 031043]. 
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  6. To overcome the reversible nature of low-Reynolds-number flow, a variety of biomimetic microrobotic propulsion schemes and devices capable of rapid transport have been developed. However, these approaches have been typically optimized for a specific function or environment and do not have the flexibility that many real organisms exhibit to thrive in complex microenvironments. Here, inspired by adaptable microbes and using a combination of experiment and simulation, we demonstrate that one-dimensional colloidal chains can fold into geometrically complex morphologies, including helices, plectonemes, lassos, and coils, and translate via multiple mechanisms that can be varied with applied magnetic field. With chains of multiblock asymmetry, the propulsion mode can be switched from bulk to surface-enabled, mimicking the swimming of microorganisms such as flagella-rotating bacteria and tail-whipping sperm and the surface-enabled motion of arching and stretching inchworms and sidewinding snakes. We also demonstrate that reconfigurability enables navigation through three-dimensional and narrow channels simulating capillary blood vessels. Our results show that flexible microdevices based on simple chains can transform both shape and motility under varying magnetic fields, a capability we expect will be particularly beneficial in complex in vivo microenvironments.

     
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