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Designing the shape of filaments by distribution of molecular motors

Bio-filaments like actin or microtubule are driven by molecular motors which exert tangential forces on their backbone. These systems can be modeled as an active polymer, a bead-spring model where each bead is endowed with an active force mimicking the effect of the molecular motor. Research has shown that distribution of molecular motors, significantly affects the shape and overall dynamics of the polymer [1,2,3]. In this project, you will perform a systematic study of the effect of active force magnitude and distribution along the filament backbone on its structure and dynamics. You will use this data as an input for a data-driven design of shape of polymers using a suitable machine learning method like reinforcement learning. The scope of this project is not limited to simulating active polymers, but allows plenty of room for method development and data-driven design based on your input and interests.

  1. Globulelike Conformation and Enhanced Diffusion of Active Polymers, Valentino Bianco, Emanuele Locatelli, and Paolo MalgarettiPhys. Rev. Lett. 121, 217802 (2018).
  2. Structure and dynamics of a self-propelled semiflexible filament, Shalabh K. Anand and Sunil P. Singh, Phys. Rev. E 98, 042501 (2018).
  3. Effects of inertia on conformation and dynamics of active filaments, M Fazelzadeh, E Irani, Z Mokhtari, S Jabbari-Farouji, arXiv:2209.07880
Contact

Dr. Sara Jabbari-Farouji s.jabbarifarouji@uva.nl at University of Amsterdam. You will be working in interdisciplinary computational soft matter lab.