simularium_readdy_models.kinesin package

Submodules

simularium_readdy_models.kinesin.kinesin_simulation module

class simularium_readdy_models.kinesin.kinesin_simulation.KinesinSimulation(parameters, record=False, save_checkpoints=False)

Bases: object

Creates a ReaDDy kinesin simulation

Params = Dict[str, float] keys: total_steps, timestep, box_size, temperature_C, viscosity, force_constant, grow_reaction_distance, attach_reaction_distance, n_cpu, tubulin_concentration, seed_n_rings, seed_n_frayed_rings_minus, seed_n_frayed_rings_plus, seed_position_offset_x, seed_position_offset_y, seed_position_offset_z, tubulin_radius, protofilament_growth_GTP_rate, protofilament_growth_GDP_rate, protofilament_shrink_GTP_rate, protofilament_shrink_GDP_rate, ring_attach_GTP_rate, ring_attach_GDP_rate, ring_detach_GTP_rate, ring_detach_GDP_rate, hydrolyze_rate, verbose

add_kinesin()

Add a kinesin

add_kinesin_constraints()

Add geometric constraints for connected kinesin particles, including bonds, angles, and repulsions, to the ReaDDy system

add_kinesin_reactions()

Add reactions to the ReaDDy system

add_kinesin_types()

Add particle and topology types for kinesin particles to the ReaDDy system

add_microtubule()

Add a microtubule

create_kinesin_system()

Create the ReaDDy system for kinesin including particle types, constraints, and reactions

simularium_readdy_models.kinesin.kinesin_util module

class simularium_readdy_models.kinesin.kinesin_util.KinesinUtil(parameters)

Bases: object

Utility functions for ReaDDy kinesin models

Parameters need to be accessible in ReaDDy callbacks which can’t be instance methods, so parameters are global

static add_angles_between_tubulins(tubulin_types, force_constant, system, util)

add angles between tubulins

static add_kinesin(position_offset, simulation)

add a kinesin to the simulation

static add_kinesin_angles_and_dihedrals(tubulin_types, force_constant, system, util)

add kinesin angles

static add_kinesin_bonds_and_repulsions(motor_types, force_constant, system, util)

add bonds between tubulins

static add_motor_bind_ATP_reaction(system)

set bound apo motor’s state to ATP (and implicitly simulate ATP binding)

static add_motor_bind_tubulin_reaction(system, rate, reaction_distance)

bind a kinesin motor in ADP state to a free tubulinB

static add_motor_release_tubulin_reaction(system)

release a bound motor from tubulin

static add_motor_tubulin_interactions(motor_types, bound_tubulin_types, tubulin_types, force_constant, system, util)

add repulsions between motors and tubulins

static add_tubulin_bonds_and_repulsions(tubulin_types, force_constant, system, util)

add bonds between tubulins

static rate_function_motor_bind_ATP(topology)

rate function for a motor binding ATP

static rate_function_motor_release_tubulin(topology)

rate function for a bound motor releasing from tubulin

static reaction_function_cleanup_release_tubulin(topology)

cleanup after releasing a bound motor from tubulin

static reaction_function_motor_bind_ATP(topology)

set bound apo motor’s state to ATP (and implicitly simulate ATP binding)

static reaction_function_motor_bind_tubulin(topology)

bind a kinesin motor in ADP state to a free tubulinB

static reaction_function_motor_release_tubulin(topology)

release a bound motor from tubulin

static set_kinesin_state(topology, recipe, from_motor_state, to_motor_state)

change the state of a motor and update the kinesin state to match

for a dictionary of types and radii [nm]

returns dictionary mapping all types to radii

simularium_readdy_models.kinesin.kinesin_util.set_parameters(p)

Module contents