src/link_2mon_sites.jl

MEDYAN.Link2MonSiteOne

Always returns 1.0

MEDYAN.Link2MonSiteCount

Returns link_2mon_state.chemstate.sitecount

MEDYAN.Link2MonSiteMonomerStateMatch

Returns 1.0 if the monomer states match, otherwise, returns 0.0.

• minusstate::Tuple{UInt8, UInt8, UInt8}: minus end monomer state
• plusstate::Tuple{UInt8, UInt8, UInt8}: plus end monomer state

MEDYAN.Link2MonSiteSlipBond

Models unbinding rates based on the following exponential form of Bell et al, 1978: min(k0*exp(f/f0), kmax) Where f is the magnitude of the force. So as to exponetially increase the unbinding with more force.

link_2mon_sitecount returns the unbinding rate in units of 1/s It returns k0 if the link_2mon hasn’t been minimized yet.

• f0::Float64: The charicteristic force magnitude. Units of pN
• k0::Float64: Unbinding rate at zero force. Units of 1/s
• kmax::Float64: Maximum rate. Units of 1/s

MEDYAN.Link2MonSiteMotorCatch

The catch-bond nature of myosin unbinding with multiple heads. Adopted from the results of Erdmann et al. 2013. The parallel cluster model.

As the force increases, the motor unbinding rate decreases to a minimum of k0/10

link_2mon_sitecount returns the unbinding rate in units of 1/s It returns k0 if the link2mon hasn’t been minimized yet. It assumes link2monstate.chemstate.numHeads exists for the link2mon.

• f0::Float64: single head characteristic unbinding force, units of pN/head
• onRate::Float64: single head binding rate, units of 1/s
• offRate::Float64: single head unbinding rate, units of 1/s
• β::Float64: slope of head binding, units of (head)/(pN/head)

MEDYAN.Link2MonSiteMotorStall

Models myosin walking rates from the results of Erdmann et al. 2013. The parallel cluster model.

As the motor work per step increases, its walking rate goes to zero.

Returns the walking rate of one end. The callback can then sample which end to move, or reject the move.

• fs::Float64: The stall force magnitude. Units of pN
• k0::Float64: Walking rate of one end at zero force. Units of 1/s
• α::Float64: Positive dimensionless parameter defining the steepness of the curve, smaller is more steep, if α is inf, the curve is linear
• walking_direction::Int32: Motor walking direction, +1 is towards plus end, -1 is towards minus end
• isminusend::Bool: which motor end does this represent