MEDYAN Publications

This page lists publications using MEDYAN in chronological order.


  1. Carlos Floyd, Haoran Ni, Ravinda Gunaratne, Radek Erban, Garegin A. Papoian (2022). On Stretching, Bending, Shearing and Twisting of Actin Filaments I: Variational Models. [Article]
  2. Aravind Chandrasekaran, Akanni Clarke, Philip McQueen, Hsiao Yu Fang, Garegin A. Papoian, Edward Giniger. Computational simulations reveal that Abl activity controls cohesiveness of actin networks in growth cones (2022). Molecular Biology of the Cell. [Article]
  3. Maria-Veronica Ciocanel, Aravind Chandrasekaran, Carli Mager, Qin Ni, Garegin A. Papoian, Andrana Dawes (2022). Simulated actin reorganization mediated by motor proteins. PLOS Computational Biology. [Article]
  4. 2021

  5. Carlos Floyd, Herbert Levine, Christopher Jarzynski, Garegin A Papoian (2021). Understanding cytoskeletal avalanches using mechanical stability analysis. PNAS. [Article]
  6. Haoran Ni, Garegin A Papoian (2021). Membrane-MEDYAN: simulating deformable vesicles containing complex cytoskeletal networks. JPCB. [Article]
  7. Carlos Floyd, Aravind Chandresekaran, Haoran Ni, Qin Ni, Garegin A Papoian (2021). Segmental Lennard-Jones Interactions for Semi-flexible Polymer Networks. Molecular Physics. [Article]
  8. 2020

  9. Xiaona Li, Qin Ni, Xiuxiu He, Jun Kong, Soon-Mi Lim, Garegin A. Papoian, Jerome P Trzeciakowski, Andreea Trache and Yi Jiang (2020). Tensile force-induced cytoskeletal remodeling: Mechanics before chemistry. PLOS Comp Biol. [Article]
  10. C Floyd, GA Papoian and C Jarzynski (2020). Gibbs free energy change of a discrete chemical reaction event. JCP. [Article]
  11. 2019

  12. Q Ni and GA Papoian (2019). Turnover versus treadmilling in actin network assembly and remodeling. Cytoskeleton. [Article]
  13. A Chandrasekaran, A Upadhyaya and GA Papoian (2019). Remarkable structural transformations of actin bundles are driven by their initial polarity, motor activity, crosslinking, and filament treadmilling. PLoS Comp Bio. [Article]
  14. C Floyd, GA Papoian and C Jarzynski (2019). Quantifying dissipation in actomyosin networks. Interface Focus. [Article]
  15. 2018

  16. JE Komianos and GA Papoian (2018). Stochastic Ratcheting on a Funneled Energy Landscape Is Necessary for Highly Efficient Contractility of Actomyosin Force Dipoles. Phys Rev X. doi:10.1103/PhysRevX.8.021006
  17. 2017

  18. C Floyd, C Jarzynski and GA Papoian (2017). Low-dimensional manifold of actin polymerization dynamics. New Journal of Physics. [Article]
  19. 2016

  20. K Popov, JE Komianos and GA Papoian (2016) MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks. PLoS Comput Biol 12(4): e1004877. doi:10.1371/journal.pcbi.1004877