TABLE I.

Parameters used in CyLaKS.

	Description	Value	Notes
General
k B T	Thermal energy	4.1 pN·nm	Room temperature
η	Fluid viscosity	0.1 pN·s·μm−2	100 times more viscous than water
t	Total simulation time	5 – 180 min	Longer time for lower protein density
t e	Pre-equilibration time	100 s	Time before equilibration status is checked
t c	Equilibration check interval	10 s	Size of data window for statistics
t s	Data snapshot interval	0.01 – 0.1 s	Time between data output
dt	Timestep	2 × 10−5 s	Time that passes each KMC step
Microtubules
L	Length	0.1 – 20 μm	Experimental values
R	Radius	12.5 nm	[97]
Δ	Site size	8 nm	[97]
N BD	BD steps per KMC step	10	Ensures stable microtubule movement
Crosslinkers
ϵ	Neighbor-neighbor energy	2.3 kBT	Estimated from PRC1 binding curve [wildenberg]
k on	Per-site binding rate	2.4 × 10−4 nM−1s−1	From koff,1 and measured Kd [98]
c	Bulk concentration	0.2 – 5.0 nM	—
c eff	Effective concentration of second head while singly bound	2.5 × 104 nM	Assumes that the second head can explore a half-sphere of radius 32 nm
k off,1	Singly bound off rate	0.14 s−1	From measured lifetime of t1/2 = 7 s [98]
k off,2	Doubly bound off rate	0.014 s−1	Set to enhance overlap occupancy [wildenberg]
D 1	Singly bound diffusivity	0.13 $\mu {\mathrm{m}}^2{\mathrm{s}}^{-1}$
D 2	Doubly bound diffusivity	0.065 $\mu {\mathrm{m}}^2{\mathrm{s}}^{-1}$	Set to match experiment [wildenberg]
r 0	Crosslinker length	32 nm	[45]
k s	Crosslinker spring constant	0.45 pN·nm−1	[99]
Motors
ϵ	Neighbor-neighbor energy	1.6 or 0 kBT	Toggles short-range interactions on or off [34]
D	Quadratic potential cutoff	8 or 0 μm	Toggles long-range interactions on or off [34]
E 0	Quadratic potential strength	0.95 kBT	[34]
E*	Quadratic potential ceiling	4.75 kBT	[34]
k on	Per-site binding rate	3.6 × 10−4 nM−1s−1	[34]
c	Bulk concentration	0.002 – 6.0 nM	—
c eff	Effective concentration of second head while singly bound	4 × 106 nM	Assumes that the second head can explore a quarter-sphere of radius 7.5 nm [34]
k ATP	ATP binding rate	5000 s−1	Assumes 2 mM ATP [86]
k hydro	ATP hydrolysis rate	95 or 110 s−1	Sets velocity to 600 or 800 nm/s to model Kif4A or kinesin-1, respectively [34, 86]
k off,1	Singly bound off rate	8 or 10 s−1	Sets processivity to 1.5 or 1.2 μm to model Kif4A or kinesin-1, respectively [34, 86]
k off,2	Doubly bound off rate	260 s−1	[86]
F int	Internal necklinker tension	26 pN	[86]
δ off,1	Singly bound distance parameter for unbinding (docked)	0.6 nm	[86]
δ off,2	Doubly bound distance parameter for unbinding (rear head)	0.13 or 0.35 nm	For Kif4A or kinesin-1, respectively [34, 86]
δ ATP	ATP binding distance parameter	1.2 or 4.6 nm	For Kif4A or kinesin-1, respectively [34, 86]