Model

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