VECTOR

Phase field simulation codes for "Condensate interfacial forces reposition DNA loci and probe chromatin viscoelasticity" by Amy R. Strom*, Yoonji Kim*, Hongbo Zhao, Yi-Che Chang, Natalia D. Orlovsky, Andrej Košmrlj, Cornelis Storm, Clifford P. Brangwynne

• To perform simulations using different viscoelasticity models, use the script VECTOR_study.m. In VECTOR_study.m, users may run the base case using the Newtonian model by setting run_base_case = true. The base case simulation consists of three steps:

  1. equilibration from the initial condition when the light is off
  2. equilibriation with the light on, until the Corelet droplet forms and merges into one
  3. turn off the light.

• To run other other viscoelastic models, set run_base_case = false and set study to the name of the viscoelastic model (see VECTOR_study.m for details). These studies use the end of the second step as the initial condition, which is saved in data/initial_condition.mat and will be loaded automatically. The simulation results for the coordinates of the telomere loci and forces over time are saved in data/yadd_* User can use VECTOR_package.m to generate visualizations of the simulation results.

• The partial differential equations (PDEs) are solved using finite differencing. Time integration is done using the implicit method via Matlab's ode15s where linear equations are solved using the direct method. The jacobian is an estimate of the full jacobian based on the block diagonals of the concentration field and the telomere degrees of freedom respectively while setting the off block diagonals to zero. Users are encouraged to use iterative (Krylov) method which requires modification of ode15s and can substantially speed up the simulations.