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  1. Traveling Waves Enhance Transport during Cytoplasmic Streaming in Drosophila Oogenesis

    Publication
    Cytoplasmic streaming is believed crucial to large developing cells, such as oocytes, where flow provides a much faster route to transport and mixing of cellular components than molecular …

  2. A stabilized finite element formulation for simulating ordered arrays of immersed flexible fibers with applications in cellular mechanics

    Publication
    We present a new computational tool for the simulation of aligned assemblies of thin, bendable, but inextensible fibers immersed in a linear Stokes fluid. Such systems are of …

  3. A fully adaptive, high-order, fast Poisson solver for complex two-dimensional geometries

    Publication
    We present a new framework for the fast solution of inhomogeneous elliptic boundary value problems in domains with smooth boundaries. High-order solvers based on adaptive box codes …

  4. Computational tools for cellular scale biophysics

    Publication
    Mathematical models are indispensable for disentangling the interactions through which biological components work together to generate the forces and flows that position, mix, and distribute proteins, nutrients, and …

  5. Self-organized intracellular twisters

    Publication
    Life in complex systems, such as cities and organisms, comes to a standstill when global coordination of mass, energy and information flows is disrupted. Global coordination is no …

  6. Conformations, correlations, and instabilities of a flexible fiber in an active fluid

    Publication
    Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered …

  7. Confirmations, correlatons and instabilities of a flexible fiber in an active fluid

    Publication
    Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered …

  8. Quadrature by fundamental solutions: kernel-independent layer potential evaluation for large collections of simple objects

    Publication
    Well-conditioned boundary integral methods for the solution of elliptic boundary value problems (BVPs) are powerful tools for static and dynamic physical simulations. When there are many close …

  9. A fast Chebyshev method for the Bingham closure with application to active nematic suspensions

    Publication
    Continuum kinetic theories provide an important tool for the analysis and simulation of particle suspensions. When those particles are anisotropic, the addition of a particle orientation vector to …

  10. Spectrally accurate solutions to inhomogeneous elliptic PDE in smooth geometries using function intension

    Publication
    We present a spectrally accurate embedded boundary method for solving linear, inhomogeneous, elliptic partial differential equations (PDE) in general smooth geometries, focusing in this manuscript on the Poisson …

  11. Thermodynamically consistent coarse-graining of polar active fluids

    Publication
    We introduce a closure model for coarse-grained kinetic theories of polar active fluids. Based on a thermodynamically consistent, quasi-equilibrium approximation of the particle distribution function, the …

  12. Hyperuniformity and phase enrichment in vortex and rotor assemblies

    Publication
    Ensembles of particles rotating in a two-dimensional fluid can exhibit chaotic dynamics yet develop signatures of hidden order. Such "rotors" are found in the natural world spanning …

  13. A fast Chebyshev method for the Bingham closure with application to active nematic suspensions

    Publication
    Continuum kinetic theories provide an important tool for the analysis and simulation of particle suspensions. When those particles are anisotropic, the addition of a particle orientation vector to …

  14. The many behaviors of deformable active droplets

    Publication
    Active fluids consume fuel at the microscopic scale, converting this energy into forces that can drive macroscopic motions over scales far larger than their microscopic constituents. In some …

  15. Swirling Instability of the Microtubule Cytoskeleton

    Publication
    In the cellular phenomena of cytoplasmic streaming, molecular motors carrying cargo along a network of microtubules entrain the surrounding fluid. The piconewton forces produced by individual motors are …

  16. Stoichiometric interactions explain spindle dynamics and scaling across 100 million years of nematode evolution

    Publication
    The spindle shows remarkable diversity, and changes in an integrated fashion, as cells vary over evolution. Here, we provide a mechanistic explanation for variations in the first mitotic …

  17. Rotating Membrane Inclusions Crystallize Through Hydrodynamic and Steric Interactions

    Publication
    We show that rotating membrane inclusions can crystallize due to combined hydrodynamic and steric interactions. Alone, steric repulsion of unconfined particles, even with thermal fluctuations, does not lead …

  18. Convergent solutions of Stokes Oldroyd-B boundary value problems using the Immersed Boundary Smooth Extension (IBSE) method

    Publication
    The Immersed Boundary (IB) method has been widely used to solve fluid-structure interaction problems, including those where the structure interacts with polymeric fluids. In this paper, we …

  19. Fast crystallization of rotating membrane proteins

    Publication
    We examine the interactions between actively rotating proteins moving in a membrane. Experimental evidence suggests that such rotor proteins, like the ATP synthases of the inner mitochondrial membrane …

  20. Coarse-graining the dynamics of immersed and driven fiber assemblies

    Publication
    An important class of fluid-structure problems involve the dynamics of ordered arrays of immersed, flexible fibers. While specialized numerical methods have been developed to study fluid-fiber …