Computational Mathematics and Scientific Computing Seminar

Rods and springs: large scale computational mechanics on active cytoskeletal assembly

Speaker: Wen Yan, Biophysical Modeling, CCB, Flatiron Institute

Location: Warren Weaver Hall 1302

Date: March 4, 2022, 10 a.m.


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 basic biological functions. Simulation of cytoskeletal assemblies is an important tool for modeling cellular processes and understanding their surprising material properties. Here we present a computational mechanics view of the cytoskeletal assembly, where we model bio-filaments as rods and motor crosslinkers as Hookean springs. We developed a new geometric constraint algorithm to break the timestep stability limit imposed by conventional potential energy methods. We implement this algorithm as aLENS, which efficiently utilizes modern HPC resources and scales millions of objects to more than 1000 cores. We demonstrate the accuracy and application of aLENS with examples of liquid crystal and self-contracting and self-buckling cytoskeletal bundles. We further discuss various extensions of our computational approach to include more capabilities.