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