Brownian dyanmics simulation for a polymer in shear flow developed to model von Willebrand factor by Hans Bergal, Darren Yang, and Wesley Wong
Untethered LJ simulation - Lennard Jones polymer without any surface with hydrodynamics provided from Rotne-Prager-Yamakawa mobility tensor Tethered LJ simulation - Lennard Jones polymer with one bead attached to surface with hydrodynamics provided from Rotne-Prager-Blake mobility tensor
These simulations were used in the publication "Conformation of von Willebrand factor in shear flow revealed with stroboscopic single-molecule imaging" https://ashpublications.org/blood/article/doi/10.1182/blood.2022016969/486450/Conformation-of-von-Willebrand-factor-in-shear
Tethered Self-Associating polymer - Includes a Lennard Jones potential term and a Self-Associating term which allows beads to form strong bonds with other beads based on a monte carlo update step. First bead is attached to the surface with hydrodynamics provided from Rotne-Prager-Blake mobility tensor-- currently unpublished.
Simulation and running details can be found in each respective folder