In FiberSim, a model file defines the structure and the biophysical proporties of a the sarcomeric system that will be simulated.

Level Parameter Units Comments
muscle no_of_half_sarcomeres None Integer defining the number of half-sarcomeres in series
  no_of_myofibrils None Currently, must be 1
  sc_k_stiff N m-1 Stiffness of an optional series elastic component. Assumed to be infinite if not defined
  initial_hs_length nm Initial length of half-sarcomere(s)
  prop_fibrosis None Proportion of cross-section occupied by fibrosis
  prop_myofilaments None Proportion of cross-section that is not fibrosis that is occupied by myofilaments
  m_filament_density m-2 The number of thick filaments per m2 in a myofilament
Level Parameter Units Comments
lattice_parameters viscosity N m-2 (nm half-sarcomere-1)-1 Passive viscous drag between myofilaments
Level Parameter Units Comments
thick_structure m_n None Integer defining the number of thick filaments to simulate. Must be an integer squared (4, 9, 16, etc. up to 196). Larger numbers produce smoother traces but take longer to simulate.
  m_crowns_per_filament None Integer defining the number of crowns per thick filament
  m_myosin_hubs_per_crown None Integer defining the number of hubs per crown. Currently must be 2 for myosin dimers.
  m_inter_crown_rest_length nm Distance between crowns in an unstressed thick filament
  m_lambda nm Length of the thick filament bare zone
  m_starting_angle degrees Orientation of the first hub
  m_inter_crown_twist degrees Angular twist between crowns
  m_within_hub_twist degrees Angular twist between heads in a hub