aLENS (a Living Ensemble Simulator) is a powerful simulation framework for studying the cytoskeleton — a dynamic network of polymer filaments, molecular motors, and other crosslinking proteins that drive essential biological processes in cells. It excels at modeling large-scale cytoskeletal assemblies, helping researchers explore how motor proteins, thermal fluctuations, mechanical stresses, and spatial confinement shape system behavior.

aLENS is a hybrid Brownian Dynamics / kinetic Monte Carlo simulation of

  • Rigid rods and spheres
  • Coupled collision-spring dynamics with steric interactions enforced by a complementarity-based method
  • Thermodynamically accurate motor/crosslinker kinetics
  • Parallel computing for large systems with tens to hundreds of thousands of particles

Read more about aLENS here and get started on the GitHub.

SkellySim (Cytoskeleton Simulator) is a high-performance application for simulating cellular components such as flexible filaments, motor proteins, and arbitrary rigid bodies immersed in fluid environments like the cytoplasm. It is designed to be highly scalable, capable of both OpenMP and MPI style parallelism, while using the efficient STKFMM/PVFMM libraries for hydrodynamic resolution.

Core Features:

  • Flexible filaments with slender body hydrodynamics, such as microtubules
  • Rigid bodies, such as organelles or microtubule organizing centers
  • Periphery, a smooth/convex containing volume, such as the cell boundary
  • Full hydrodynamic simulation of the above via a hybrid backward implicit/explicit Euler scheme

Read more about SkellySim here and get started on the GitHub.