Colloidal hard spheres: Triumphs, challenges, and mysteries

CP Royall, P Charbonneau, M Dijkstra, J Russo… - Reviews of Modern …, 2024 - APS
The simplicity of hard spheres as a model system is deceptive. Although the particles
interact solely through volume exclusion, that nevertheless suffices for a wealth of static and …

Computational tools for cellular scale biophysics

DB Stein, MJ Shelley - Current Opinion in Cell Biology, 2024 - Elsevier
Mathematical models are indispensable for disentangling the interactions through which
biological components work together to generate the forces and flows that position, mix, and …

Toward the cellular-scale simulation of motor-driven cytoskeletal assemblies

W Yan, S Ansari, A Lamson, MA Glaser, R Blackwell… - Elife, 2022 - elifesciences.org
The cytoskeleton–a collection of polymeric filaments, molecular motors, and crosslinkers–is
a foundational example of active matter, and in the cell assembles into organelles that guide …

[HTML][HTML] Efficient convergent boundary integral methods for slender bodies

D Malhotra, A Barnett - Journal of Computational Physics, 2024 - Elsevier
The interaction of fibers in a viscous (Stokes) fluid plays a crucial role in industrial and
biological processes, such as sedimentation, rheology, transport, cell division, and …

Integral-based spectral method for inextensible slender fibers in Stokes flow

O Maxian, A Mogilner, A Donev - Physical Review Fluids, 2021 - APS
Every animal cell is filled with a cytoskeleton, a dynamic gel made of inextensible fibers,
such as microtubules, actin fibers, and intermediate filaments, all suspended in a viscous …

Fast simulation of particulate suspensions enabled by graph neural network

Z Ma, Z Ye, W Pan - Computer Methods in Applied Mechanics and …, 2022 - Elsevier
Predicting the dynamic behaviors of particles in suspension subject to hydrodynamic
interaction (HI) and external drive can be critical for many applications. By harvesting …

Shape deformation, disintegration, and coalescence of suspension drops: Efficient simulation enabled by graph neural networks

Z Ma, W Pan - International Journal of Multiphase Flow, 2024 - Elsevier
Understanding the behaviors of suspension drops (particle swarms) as they settle in a
viscous fluid holds significant importance across various applications. Due to hydrodynamic …

A design framework for actively crosslinked filament networks

S Fürthauer, DJ Needleman… - New Journal of Physics, 2021 - iopscience.iop.org
Living matter moves, deforms, and organizes itself. In cells this is made possible by networks
of polymer filaments and crosslinking molecules that connect filaments to each other and …

Driven dynamics in dense suspensions of microrollers

B Sprinkle, EB Van Der Wee, Y Luo, MM Driscoll… - Soft Matter, 2020 - pubs.rsc.org
We perform detailed computational and experimental measurements of the driven dynamics
of a dense, uniform suspension of sedimented microrollers driven by a magnetic field …

Thermodynamically consistent coarse-graining of polar active fluids

S Weady, DB Stein, MJ Shelley - Physical Review Fluids, 2022 - APS
We introduce a closure model for coarse-grained kinetic theories of polar active fluids.
Based on a quasiequilibrium approximation of the particle distribution function, the model …