arXiv subjects

Eric Keaveny

Publications and source records attributed to Eric Keaveny.

5 recordsLinked to original sources

arXiv2024

Bifurcations and nonlinear dynamics of the follower force model for active filaments

Biofilament-motor protein complexes are ubiquitous in biology and drive the transport of cargo vital for many fundamental cellular processes. As they move, motor proteins exert compressive forces on the filaments to which they are attached, leading to buckling and a subsequent range of dynamics. The follower force model, in which a single compressive force is imposed at the filament tip, is the standard and most basic model for an elastic filament, such as a microtubule, driven by a motor protein. Depending on the force value, one can observe different states including whirling, beating and writhing, though the bifurcations giving rise to these states are not completely understood. In this paper, we utilise techniques from computational dynamical systems to determine and characterise these bifurcations. We track emerging time-periodic branches and identify new, quasiperiodic states. We investigate the effect of filament slenderness on the bifurcations and, in doing so, present a comprehensive overview of the dynamics which emerge in the follower force model.

physics.bio-ph↗

arXiv2019

Spontaneous onset of convection in a uniform phoretic channel

Phoretic mechanisms, whereby gradients of chemical solutes induce surface-driven flows, have recently been used to generate directed propulsion of patterned colloidal particles. When the chemical solutes diffuse slowly, an instability further provides active but isotropic particles with a route to self-propulsion by spontaneously breaking the symmetry of the solute distribution. Here we show theoretically that, in a mechanism analogous to Bénard-Marangoni convection, phoretic phenomena can create spontaneous and self-sustained wall-driven mixing flows within a straight, chemically-uniform active channel. Such spontaneous flows do not result in any net pumping for a uniform channel but greatly modify the distribution of transport of the chemical solute. The instability is predicted to occur for a solute Péclet number above a critical value and for a band of finite perturbation wavenumbers. We solve the perturbation problem analytically to characterize the instability, and use both steady and unsteady numerical computations of the full nonlinear transport problem to capture the long-time coupled dynamics of the solute and flow within the channel.

physics.flu-dyn↗

arXiv2017

A fluctuating boundary integral method for Brownian suspensions

We present a fluctuating boundary integral method (FBIM) for overdamped Brownian Dynamics (BD) of two-dimensional periodic suspensions of rigid particles of complex shape immersed in a Stokes fluid. We develop a novel approach for generating Brownian displacements that arise in response to the thermal fluctuations in the fluid. Our approach relies on a first-kind boundary integral formulation of a mobility problem in which a random surface velocity is prescribed on the particle surface, with zero mean and covariance proportional to the Green's function for Stokes flow (Stokeslet). This approach yields an algorithm that scales linearly in the number of particles for both deterministic and stochastic dynamics, handles particles of complex shape, achieves high order of accuracy, and can be generalized to three dimensions and other boundary conditions. We show that Brownian displacements generated by our method obey the discrete fluctuation-dissipation balance relation (DFDB). Based on a recently-developed Positively Split Ewald method [A. M. Fiore, F. Balboa Usabiaga, A. Donev and J. W. Swan, J. Chem. Phys., 146, 124116, 2017], near-field contributions to the Brownian displacements are efficiently approximated by iterative methods in real space, while far-field contributions are rapidly generated by fast Fourier-space methods based on fluctuating hydrodynamics. FBIM provides the key ingredient for time integration of the overdamped Langevin equations for Brownian suspensions of rigid particles. We demonstrate that FBIM obeys DFDB by performing equilibrium BD simulations of suspensions of starfish-shaped bodies using a random finite difference temporal integrator.

math.NA↗

arXiv2015

Large-scale simulation of steady and time-dependent active suspensions with the force-coupling method

We present a new development of the force-coupling method (FCM) to address the accurate simulation of a large number of interacting micro-swimmers. Our approach is based on the squirmer model, which we adapt to the FCM framework, resulting in a method that is suitable for simulating semi-dilute squirmer suspensions. Other effects, such as steric interactions, are considered with our model. We test our method by comparing the velocity field around a single squirmer and the pairwise interactions between two squirmers with exact solutions to the Stokes equations and results given by other numerical methods. We also illustrate our method's ability to describe spheroidal swimmer shapes and biologically-relevant time-dependent swimming gaits. We detail the numerical algorithm used to compute the hydrodynamic coupling between a large collection ($10^4-10 ^5$) of micro-swimmers. Using this methodology, we investigate the emergence of polar order in a suspension of squirmers and show that for large domains, both the steady-state polar order parameter and the growth rate of instability are independent of system size. These results demonstrate the effectiveness of our approach to achieve near continuum-level results, allowing for better comparison with experimental measurements while complementing and informing continuum models.

cond-mat.soft↗

arXiv2010

Locomotion of C. elegans in Structured Environments

Undulatory locomotion of microorganisms like soil-dwelling worms and spermatozoa, in structured environments, is ubiquitous in nature. They navigate complex environments consisting of fluids and obstacles, negotiating hydrodynamic effects and geometrical constraints. Here, we show fluid dynamics videos of experiments and simulations of {\textit {C. elegans}} moving in an array of micro-pillars. In addition, we show a video of transition from swimming to crawling in drop of {\textit {C. elegans}}, where the fluid is wicking into agar.

physics.flu-dyn↗