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 m^{2} 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