MEDYAN Publications

This page lists publications using MEDYAN in chronological order.

    Preprint

  1. Haoran Ni, Garegin A Papoian (2021). Membrane-MEDYAN: Simulating Deformable Vesicles Containing Complex Cytoskeletal Networks. [Article]
  2. Carlos Floyd, Herbert Levine, Christopher Jarzynski, Garegin A Papoian (2020). Hessian Analysis Enables Prediction of Cytoquake Occurrence. [Article]
  3. 2021

  4. Carlos Floyd, Aravind Chandresekaran, Haoran Ni, Qin Ni, Garegin A Papoian (2021). Segmental Lennard-Jones Interactions for Semi-flexible Polymer Networks. Molecular Physics. [Article]
  5. 2020

  6. 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]
  7. C Floyd, GA Papoian and C Jarzynski (2020). Gibbs free energy change of a discrete chemical reaction event. JCP. [Article]
  8. 2019

  9. Q Ni and GA Papoian (2019). Turnover versus treadmilling in actin network assembly and remodeling. Cytoskeleton. [Article]
  10. 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]
  11. C Floyd, GA Papoian and C Jarzynski (2019). Quantifying dissipation in actomyosin networks. Interface Focus. [Article]
  12. 2018

  13. 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
  14. 2017

  15. C Floyd, C Jarzynski and GA Papoian (2017). Low-dimensional manifold of actin polymerization dynamics. New Journal of Physics. [Article]
  16. 2016

  17. 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