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Barbed binding site #32

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blairlyons wants to merge 11 commits into from
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Barbed binding site #32

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eefc084
obstacle can have nonzero diff coeff and is confined to a box along t…
Feb 15, 2025
11c1e26
obstacle position can be set at a given stride
Feb 15, 2025
223c4d0
add repulsions for free actins
Feb 15, 2025
4635809
add position_obstacle_stride to default parameters
Feb 15, 2025
1a1528f
WIP create membrane with a lattice of two sheets of particles, TODO c…
Mar 21, 2025
36966f6
membrane tested with readdy, TODO debug box potentials
Mar 22, 2025
2607adc
fixed edge box potentials
Mar 24, 2025
f6031be
add repulsions between actin and membrane
Mar 24, 2025
fc01576
add an extra box potential (that can be used as a membrane obstacle)
Mar 28, 2025
0781c0c
binding site particle to define a local binding pocket for barbed actin
May 6, 2025
fb12044
fix reaction error
May 19, 2025
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13 changes: 12 additions & 1 deletion simularium_readdy_models/actin/actin_generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -449,6 +449,7 @@ def _get_main_monomers_for_fiber(
pointed_actin_number,
particles={},
longitudinal_bonds=True,
barbed_binding_site=False,
):
"""
get the main actins for a fiber (i.e. no branches or arps).
Expand Down Expand Up @@ -549,8 +550,14 @@ def _get_main_monomers_for_fiber(
# remove "mid" from second actin
ActinGenerator._remove_mid_from_actin(particle_ids[1], particles)
actin_arp_ids = None
if barbed_binding_site and len(particle_ids) > 1:
particles = ActinGenerator._set_particle_type_name(
"actin#barbed_ATP_" ,
particle_ids[len(particle_ids) - 2],
particles,
)
particles = ActinGenerator._set_particle_type_name(
"actin#barbed_ATP_",
"actin#barbed_ATP_" if not barbed_binding_site else "binding_site#" ,
particle_ids[len(particle_ids) - 1],
particles,
)
Expand All @@ -565,6 +572,7 @@ def _get_monomers_for_fiber(
pointed_actin_number,
particles={},
longitudinal_bonds=True,
barbed_binding_site=False,
):
"""
get the main actins for a fiber as well as any bound arps and daughter fibers.
Expand All @@ -581,6 +589,7 @@ def _get_monomers_for_fiber(
pointed_actin_number,
particles,
longitudinal_bonds,
barbed_binding_site,
)
daughter_particle_ids = []
all_actin_arp_ids = []
Expand Down Expand Up @@ -800,6 +809,7 @@ def get_monomers(
use_uuids=True,
start_normal=None,
longitudinal_bonds=True,
barbed_binding_site=False,
):
"""
get all the monomer data for the (branched) fibers in fibers_data.
Expand Down Expand Up @@ -836,6 +846,7 @@ def get_monomers(
np.zeros(3),
1,
longitudinal_bonds=longitudinal_bonds,
barbed_binding_site=barbed_binding_site,
)
result["topologies"][ActinGenerator._get_next_monomer_id()] = {
"type_name": "Actin-Polymer",
Expand Down
107 changes: 91 additions & 16 deletions simularium_readdy_models/actin/actin_simulation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,13 @@
import numpy as np
import readdy

from ..common import ReaddyUtil
from ..common import (
ReaddyUtil,
add_membrane_particle_types,
add_membrane_constraints,
init_membrane,
all_membrane_particle_types
)
from .actin_structure import ActinStructure
from .actin_util import ActinUtil

Expand Down Expand Up @@ -110,7 +116,14 @@ def add_particle_types(self):
self.actin_util.add_actin_types(self.system, actin_diffCoeff)
self.actin_util.add_arp23_types(self.system, arp23_diffCoeff)
self.actin_util.add_cap_types(self.system, cap_diffCoeff)
self.system.add_species("obstacle", 0.0)
self.system.topologies.add_type("Obstacle")
self.system.add_topology_species("obstacle", self._parameter("obstacle_diff_coeff"))
if self._parameter("add_membrane"):
add_membrane_particle_types(
self.system, self._parameter("membrane_particle_radius"), temperature, viscosity
)
if self._parameter("barbed_binding_site"):
self.actin_util.add_binding_site_types(self.system, actin_diffCoeff)

def add_constraints(self):
"""
Expand All @@ -120,6 +133,7 @@ def add_constraints(self):
util = ReaddyUtil()
longitudinal_bonds = bool(self._parameter("longitudinal_bonds"))
only_linear_actin = bool(self._parameter("only_linear_actin_constraints"))
actin_constraints = bool(self._parameter("actin_constraints"))
# force constants
actin_angle_force_constant = float(self._parameter("angles_force_constant"))
actin_dihedral_force_constant = float(
Expand All @@ -132,16 +146,17 @@ def add_constraints(self):
longitudinal_bonds,
float(self._parameter("bonds_force_multiplier")),
)
self.actin_util.add_filament_twist_angles(
actin_angle_force_constant, self.system, util, longitudinal_bonds
)
self.actin_util.add_filament_twist_dihedrals(
actin_dihedral_force_constant,
self.system,
util,
longitudinal_bonds,
only_linear_actin,
)
if actin_constraints:
self.actin_util.add_filament_twist_angles(
actin_angle_force_constant, self.system, util, longitudinal_bonds
)
self.actin_util.add_filament_twist_dihedrals(
actin_dihedral_force_constant,
self.system,
util,
longitudinal_bonds,
only_linear_actin,
)
if not only_linear_actin:
# branch junction
self.actin_util.add_branch_bonds(self.system, util)
Expand Down Expand Up @@ -170,8 +185,41 @@ def add_constraints(self):
actin_actin_repulsion_potentials=True,
longitudinal_bonds=longitudinal_bonds,
)
self.actin_util.add_repulsions_with_actin(
["obstacle"],
self._parameter("obstacle_radius"),
ActinUtil.DEFAULT_FORCE_CONSTANT,
self.system,
util
)
# box potentials
self.actin_util.add_monomer_box_potentials(self.system)
self.actin_util.add_obstacle_box_potential(self.system)
self.actin_util.add_extra_box(self.system)
# membrane
if self._parameter("add_membrane"):
add_membrane_constraints(
self.system,
np.array([
float(self._parameter("membrane_center_x")),
float(self._parameter("membrane_center_y")),
float(self._parameter("membrane_center_z")),
]),
np.array([
float(self._parameter("membrane_size_x")),
float(self._parameter("membrane_size_y")),
float(self._parameter("membrane_size_z")),
]),
self._parameter("membrane_particle_radius"),
self._parameter("box_size")
)
self.actin_util.add_repulsions_with_actin(
all_membrane_particle_types(),
self._parameter("membrane_particle_radius"),
ActinUtil.DEFAULT_FORCE_CONSTANT,
self.system,
util
)

def add_reactions(self):
"""
Expand All @@ -198,6 +246,8 @@ def add_reactions(self):
self.actin_util.add_cap_unbind_reaction(self.system)
if self.do_pointed_end_translation():
self.actin_util.add_translate_reaction(self.system)
if self._parameter("position_obstacle_stride") > 0:
self.actin_util.add_position_obstacle_reaction(self.system)

def do_pointed_end_translation(self):
result = self._parameter("displace_pointed_end_tangent") or self._parameter(
Expand Down Expand Up @@ -330,19 +380,44 @@ def add_obstacles(self):
"""
Add obstacle particles.
"""
if not self._parameter("add_obstacles"):
return
n = 0
while f"obstacle{n}_position_x" in self.parameters:
self.simulation.add_particle(
type="obstacle",
position=[
self.simulation.add_topology(
"Obstacle",
["obstacle"],
np.array([[
float(self._parameter(f"obstacle{n}_position_x")),
float(self._parameter(f"obstacle{n}_position_y")),
float(self._parameter(f"obstacle{n}_position_z")),
],
]])
)
n += 1
if n > 0:
print(f"Added {n} obstacle(s).")

def add_membrane(self):
"""
Add membrane types and particles.
"""
if not self._parameter("add_membrane"):
return
init_membrane(
self.simulation,
np.array([
float(self._parameter("membrane_center_x")),
float(self._parameter("membrane_center_y")),
float(self._parameter("membrane_center_z")),
]),
np.array([
float(self._parameter("membrane_size_x")),
float(self._parameter("membrane_size_y")),
float(self._parameter("membrane_size_z")),
]),
self._parameter("membrane_particle_radius"),
self._parameter("box_size")
)

def add_crystal_structure_monomers(self):
"""
Expand Down
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