def set_next_state(
self,
next_state_array,
close_point_smoothness_factors,
x_cils,
x_coas,
):
self.tpoint += self.dt
self.insert_state_array_into_system_history(next_state_array)
verts = self.curr_state[:, [parameters.x_ix, parameters.y_ix]]
edge_displacement_vectors_plus = geometry.calculate_edge_vectors(verts)
edge_lengths = geometry.calculate_vec_mags(
edge_displacement_vectors_plus)
self.curr_state[:, parameters.edge_lengths_ix] = edge_lengths
self.curr_state[:, parameters.old_x_coa_ix] = x_coas
self.curr_state[:, parameters.old_x_cil_ix] = x_cils
# ==================================
if self.tpoint == self.next_randomization_event_tpoint:
self.next_randomization_event_tpoint += 1200
# randomization event has occurred, so renew Rac kgtp rate
# multipliers
self.rac_rands = \
self.renew_rac_rands(
self.tpoint)
# store the Rac randomization factors for this timestep
self.curr_state[:, parameters.rac_rands_ix] = self.rac_rands
# ==================================
rac_acts = self.curr_state[:, parameters.rac_act_ix]
rho_acts = self.curr_state[:, parameters.rho_act_ix]
self.curr_state[:, parameters.old_x_cil_ix] = x_cils
self.curr_state[:, parameters.old_x_coa_ix] = x_coas
rac_cyto = (1 - np.sum(rac_acts) -
np.sum(self.curr_state[:, parameters.rac_inact_ix]))
rho_cyto = (1 - np.sum(rho_acts) -
np.sum(self.curr_state[:, parameters.rho_inact_ix]))
insertion_array = np.zeros(16)
insertion_array[0] = 1
self.curr_state[:,
parameters.rac_cyto_ix] = (rac_cyto * insertion_array)
self.curr_state[:,
parameters.rho_cyto_ix] = (rho_cyto * insertion_array)
sum_forces, edge_forces_plus, edge_forces_minus, uevs, rgtp_forces, \
cyto_forces, \
edge_strains, local_strains, unit_inside_pointing_vecs = \
mechanics.calculate_forces(
verts,
rac_acts,
rho_acts,
self.rest_edge_len,
self.stiffness_edge,
self.halfmax_vertex_rgtp,
self.const_protrusive,
self.const_retractive,
self.rest_area,
self.stiffness_cyto,
)
self.curr_state[:, parameters.local_strains_ix] = local_strains
edgeplus_lengths = geometry.calculate_edgeplus_lengths(verts)
avg_edge_lengths = geometry.calculate_average_edge_length_around_nodes(
edgeplus_lengths)
conc_rac_acts = chemistry.calc_concs(rac_acts, avg_edge_lengths)
conc_rho_acts = chemistry.calc_concs(rho_acts, avg_edge_lengths)
self.curr_state[:, parameters.rac_rands_ix] = self.rac_rands
kgtp_racs = chemistry.calculate_kgtp_rac(
conc_rac_acts,
self.halfmax_vertex_rgtp_conc,
self.kgtp_rac,
self.kgtp_rac_auto,
x_coas,
self.rac_rands,
x_cils,
close_point_smoothness_factors,
)
kdgtps_rac = chemistry.calculate_kdgtp_rac(
conc_rho_acts,
self.halfmax_vertex_rgtp_conc,
self.kdgtp_rac,
self.kdgtp_rho_on_rac,
x_cils,
self.halfmax_tension_inhib,
self.tension_inhib,
np.array([ls if ls > 0 else 0.0 for ls in local_strains]),
)
kdgtps_rho = chemistry.calculate_kdgtp_rho(
conc_rac_acts,
self.halfmax_vertex_rgtp_conc,
self.kdgtp_rho,
self.kdgtp_rac_on_rho,
)
kgtp_rhos = chemistry.calculate_kgtp_rho(
conc_rho_acts,
x_cils,
self.halfmax_vertex_rgtp_conc,
self.kgtp_rho,
self.kgtp_rho_auto,
)
self.curr_state[:, parameters.kgtp_rac_ix] = kgtp_racs
self.curr_state[:, parameters.kgtp_rho_ix] = kgtp_rhos
self.curr_state[:, parameters.kdgtp_rac_ix] = kdgtps_rac
self.curr_state[:, parameters.kdgtp_rho_ix] = kdgtps_rho
# update mechanics parameters
self.curr_state[:, [
parameters.sum_forces_x_ix, parameters.sum_forces_y_ix
]] = sum_forces
self.curr_state[:, [parameters.edge_forces_plus_x_ix,
parameters.edge_forces_plus_y_ix]] = \
edge_forces_plus
self.curr_state[:, [parameters.edge_forces_minus_x_ix,
parameters.edge_forces_minus_y_ix]] = \
edge_forces_minus
self.curr_state[:, [
parameters.rgtp_forces_x_ix, parameters.rgtp_forces_y_ix
]] = rgtp_forces
self.curr_state[:, [
parameters.cyto_forces_x_ix, parameters.cyto_forces_y_ix
]] = cyto_forces
self.curr_state[:, [parameters.uiv_x_ix, parameters.
uiv_y_ix]] = unit_inside_pointing_vecs
self.curr_verts = verts
def __init__(
self,
cell_group_ix,
cell_ix,
params,
dt,
):
self.cell_group_ix = cell_group_ix
self.cell_ix = cell_ix
self.num_int_steps = params["num_int_steps"]
self.dt = dt
self.tpoint = 0.0
self.num_cells = params["num_cells"]
self.tot_rac = params["tot_rac"]
self.tot_rho = params["tot_rho"]
self.curr_state = np.zeros((
16,
len(parameters.output_info_labels),
))
self.length = params["l"]
self.t = params["t"]
self.f = params["f"]
self.vertex_eta = params["vertex_eta"]
self.curr_verts = params["init_verts"]
self.radius_resting = params["cell_r"]
self.rest_edge_len = params["rest_edge_len"]
edgeplus_lengths = geometry.calculate_edgeplus_lengths(self.curr_verts)
self.init_average_edge_lengths = np.average(
geometry.calculate_average_edge_length_around_nodes(
edgeplus_lengths))
self.rest_area = params["rest_area"]
# ======================================================
self.close_zero_at = params["close_zero_at"]**2
self.close_one_at = params["close_one_at"]**2
self.kgtp_rac = params["kgtp_rac"]
self.kgtp_rac_auto = params["kgtp_rac_auto"]
self.halfmax_vertex_rgtp = params["halfmax_vertex_rgtp"]
self.halfmax_vertex_rgtp_conc = params["halfmax_vertex_rgtp_conc"]
self.kdgtp_rac = params["kdgtp_rac"]
self.kdgtp_rho_on_rac = params["kdgtp_rho_on_rac"]
self.halfmax_tension_inhib = params["halfmax_tension_inhib"]
self.tension_inhib = params["tension_inhib"]
self.k_mem_off = params["k_mem_off"]
self.k_mem_on_vertex = params["k_mem_on_vertex"]
self.diffusion_rgtp = params["diffusion_rgtp"]
# ======================================================
self.kgtp_rho = params["kgtp_rho"]
self.kgtp_rho_auto = params["kgtp_rho_auto"]
self.kdgtp_rho = params["kdgtp_rho"]
self.kdgtp_rac_on_rho = params["kdgtp_rac_on_rho"]
# ==============================================================
self.cil_mag = params["cil_mag"]
self.coa_mag = params["coa_vertex_mag"]
self.coa_distrib_exp = params["coa_distrib_exp"]
self.coa_los_penalty = params["coa_los_penalty"]
# =============================================================
self.stiffness_edge = params["stiffness_edge"]
self.stiffness_cyto = params["stiffness_cyto"]
self.const_protrusive = params["const_protrusive"]
self.const_retractive = params["const_retractive"]
# =============================================================
self.phase_var_indices = [
parameters.rac_act_ix,
parameters.rac_inact_ix,
parameters.rho_act_ix,
parameters.rho_inact_ix,
parameters.x_ix,
parameters.y_ix,
]
self.num_phase_vars = len(self.phase_var_indices)
self.total_num_phase_vars = self.num_phase_vars * \
16
self.initialize_phase_var_indices()
# =============================================================
self.rand_avg_t = params["rand_avg_t"]
self.rand_std_t = params["rand_std_t"]
self.rand_mag = params["rand_mag"]
self.num_rand_vs = params["num_rand_vs"]
self.randomization = params["randomization"]
self.rac_rands = self.renew_rac_rands(0)
self.next_randomization_event_tpoint = 1200
# =============================================================
self.all_cellwide_phase_var_indices = [
parameters.rac_cyto_ix,
parameters.rho_cyto_ix,
]
self.ode_cellwide_phase_var_indices = []
self.num_all_cellwide_phase_vars = len(
self.all_cellwide_phase_var_indices)
self.num_ode_cellwide_phase_vars = len(
self.ode_cellwide_phase_var_indices)
self.initialize_all_cellwide_phase_var_indices()
self.initialize_ode_cellwide_phase_var_indices()
# =============================================================
self.pars_indices = [
parameters.kgtp_rac_ix,
parameters.kgtp_rho_ix,
parameters.kdgtp_rac_ix,
parameters.kdgtp_rho_ix,
parameters.local_strains_ix,
parameters.old_x_cil_ix,
]
self.initialize_pars_indices()
# =============================================================
self.init_inact_rgtp = params["init_inact_rgtp"]
self.init_act_rgtp = params["init_act_rgtp"]
self.rgtp_distrib_def_for_randomization = [
"unbiased random",
0.0,
0.0,
]
self.init_rac = params["init_rac"]
self.init_rho = params["init_rho"]
def cell_dynamics(
focus_verts, tpoint, int_step, dt, writer, cell_ix, state_array,
num_cells, all_cells_verts, num_phase_vars, rac_act_ix, rest_edge_len,
rac_inact_ix, rho_act_ix, rho_inact_ix, x_ix, y_ix, kgtp_rac,
kdgtp_rac, kgtp_rho, kdgtp_rho, kgtp_rac_auto, kgtp_rho_auto,
kdgtp_rho_on_rac, kdgtp_rac_on_rho, k_mem_on_vertex, k_mem_off,
halfmax_vertex_rgtp_conc, diffusion_rgtp, vertex_eta, stiffness_edge,
halfmax_vertex_rgtp, const_protrusive, const_retractive, rest_area,
stiffness_cyto, x_coas, close_point_smoothness_factors, x_cils,
halfmax_tension_inhib, tension_inhib, rac_rands, coa_updates,
cil_updates):
phase_vars = state_array
rac_mem_active_start_ix = rac_act_ix * 16
rac_mem_active_end_ix = rac_mem_active_start_ix + 16
rac_acts = phase_vars[rac_mem_active_start_ix:rac_mem_active_end_ix]
rac_mem_inactive_start_ix = rac_inact_ix * 16
rac_mem_inactive_end_ix = rac_mem_inactive_start_ix + 16
rac_inacts = phase_vars[rac_mem_inactive_start_ix:rac_mem_inactive_end_ix]
rho_mem_active_start_ix = rho_act_ix * 16
rho_mem_active_end_ix = rho_mem_active_start_ix + 16
rho_acts = phase_vars[rho_mem_active_start_ix:rho_mem_active_end_ix]
rho_mem_inactive_start_ix = rho_inact_ix * 16
rho_mem_inactive_end_ix = rho_mem_inactive_start_ix + 16
rho_inacts = phase_vars[rho_mem_inactive_start_ix:rho_mem_inactive_end_ix]
x_start_ix = x_ix * 16
x_end_ix = x_start_ix + 16
x = phase_vars[x_start_ix:x_end_ix]
y_start_ix = y_ix * 16
y_end_ix = y_start_ix + 16
y = phase_vars[y_start_ix:y_end_ix]
poly = general_utilities.make_verts_array_given_xs_and_ys(x, y)
rac_cyto = (1 - calculate_sum(16, rac_acts) -
calculate_sum(16, rac_inacts))
rho_cyto = (1 - calculate_sum(16, rho_acts) -
calculate_sum(16, rho_inacts))
sum_forces, edge_forces_plus, edge_forces_minus, uevs, rgtp_forces, \
cyto_forces, \
edge_strains, local_strains, \
uivs = mechanics.calculate_forces(
poly,
rac_acts,
rho_acts,
rest_edge_len,
stiffness_edge,
halfmax_vertex_rgtp,
const_protrusive,
const_retractive,
rest_area,
stiffness_cyto,
)
sum_forces_x = sum_forces[:, 0]
sum_forces_y = sum_forces[:, 1]
only_tensile_local_strains = np.zeros_like(local_strains)
for i in range(16):
local_strain = local_strains[i]
if local_strain > 0:
only_tensile_local_strains[i] = local_strain
edgeplus_lengths = geometry.calculate_edgeplus_lengths(poly)
avg_edge_lengths = geometry.calculate_average_edge_length_around_nodes(
edgeplus_lengths)
conc_rac_acts = chemistry.calc_concs(rac_acts, avg_edge_lengths)
kgtps_rac = chemistry.calculate_kgtp_rac(
conc_rac_acts,
halfmax_vertex_rgtp_conc,
kgtp_rac,
kgtp_rac_auto,
x_coas,
rac_rands,
x_cils,
close_point_smoothness_factors,
)
conc_rho_acts = chemistry.calc_concs(rho_acts, avg_edge_lengths)
global_tension = np.sum(only_tensile_local_strains) / 16
if global_tension < 0.0:
global_tension = 0.0
strain_inhibition = tension_inhib * \
chemistry.hill_function3(
halfmax_tension_inhib,
global_tension
)
kdgtps_rac = chemistry.calculate_kdgtp_rac(
conc_rho_acts,
halfmax_vertex_rgtp_conc,
kdgtp_rac,
kdgtp_rho_on_rac,
x_cils,
halfmax_tension_inhib,
tension_inhib,
only_tensile_local_strains,
)
kgtps_rho = chemistry.calculate_kgtp_rho(
conc_rho_acts,
x_cils,
halfmax_vertex_rgtp_conc,
kgtp_rho,
kgtp_rho_auto,
)
kdgtps_rho = chemistry.calculate_kdgtp_rho(
conc_rac_acts,
halfmax_vertex_rgtp_conc,
kdgtp_rho,
kdgtp_rac_on_rho,
)
conc_rac_inacts = chemistry.calc_concs(rac_inacts, avg_edge_lengths)
conc_rho_inact = chemistry.calc_concs(rho_inacts, avg_edge_lengths)
rac_act_net_fluxes = chemistry.calculate_net_fluxes(
conc_rac_acts,
diffusion_rgtp,
edgeplus_lengths,
)
rac_inact_net_fluxes = chemistry.calculate_net_fluxes(
conc_rac_inacts,
diffusion_rgtp,
edgeplus_lengths,
)
rho_act_net_fluxes = chemistry.calculate_net_fluxes(
conc_rho_acts,
diffusion_rgtp,
edgeplus_lengths,
)
rho_inact_net_fluxes = chemistry.calculate_net_fluxes(
conc_rho_inact,
diffusion_rgtp,
edgeplus_lengths,
)
delta_rac_activated = np.zeros(16, dtype=np.float64)
delta_rac_inactivated = np.zeros(16, dtype=np.float64)
delta_rac_cytosol_to_membrane = np.zeros(16, dtype=np.float64)
delta_rho_activated = np.zeros(16, dtype=np.float64)
delta_rho_inactivated = np.zeros(16, dtype=np.float64)
delta_rho_cytosol_to_membrane = np.zeros(16, dtype=np.float64)
delta_x = np.zeros(16, dtype=np.float64)
delta_y = np.zeros(16, dtype=np.float64)
new_verts = np.zeros((16, 2), dtype=np.float64)
np.zeros(2, dtype=np.float64)
np.zeros(2, dtype=np.float64)
# logging.log(level=DYNAMICS_INFO,
# msg="tstep: {}, int_step: {}".format(tpoint, int_step))
# logging.log(level=DYNAMICS_INFO, msg="eta: {}".format(vertex_eta))
# logging.log(level=DYNAMICS_INFO, msg="1/eta: {}".format(1 / vertex_eta))
# for ix in focus_verts:
# logging.log(level=DYNAMICS_INFO,
# msg="rgtp_forces[{}]: {}".format(ix, rgtp_forces[ix]))
# logging.log(level=DYNAMICS_INFO,
# msg="edge_forces[{}]: {}".format(ix,
# edge_forces_plus[ix]))
# logging.log(level=DYNAMICS_INFO,
# msg="cyto_forces[{}]: {}".format(ix, cyto_forces[ix]))
# logging.log(level=DYNAMICS_INFO,
# msg="expected sum forces ({}) = {}".format(ix,
# rgtp_forces[
# ix] +
# edge_forces_plus[
# ix] +
# edge_forces_minus[
# ix] +
# cyto_forces[
# ix]))
# logging.log(level=DYNAMICS_INFO,
# msg="sum_forces[{}]: {}".format(ix, sum_forces[ix]))
poly_area = geometry.calculate_polygon_area(poly)
data = [("tpoint", tpoint),
("poly", [[float(v) for v in x] for x in poly]),
("rac_acts", [float(v) for v in rac_acts]),
("rac_inacts", [float(v) for v in rac_inacts]),
("rho_acts", [float(v) for v in rho_acts]),
("rho_inacts", [float(v) for v in rho_inacts]),
("sum_forces", [
list([float(x), float(y)])
for x, y in zip(sum_forces_x, sum_forces_y)
]), ("uivs", [[float(v) for v in x] for x in uivs]),
("rgtp_forces", [[float(v) for v in x] for x in rgtp_forces]),
("edge_forces", [[float(v) for v in x] for x in edge_forces_plus]),
("cyto_forces", [[float(v) for v in x] for x in cyto_forces]),
("kgtps_rac", [float(v) for v in kgtps_rac]),
("kdgtps_rac", [float(v) for v in kdgtps_rac]),
("kgtps_rho", [float(v) for v in kgtps_rho]),
("kdgtps_rho", [float(v) for v in kdgtps_rho]),
("x_cils", [float(v) for v in x_cils]),
("x_coas", [float(v) for v in x_coas]),
("edge_strains", [float(v) for v in local_strains]),
("avg_tens_strain", [float(global_tension)
for _ in local_strains]),
("poly_area", poly_area),
("rac_act_net_fluxes", [float(v) for v in rac_act_net_fluxes]),
("rac_inact_net_fluxes", [float(v) for v in rac_inact_net_fluxes]),
("rho_act_net_fluxes", [float(v) for v in rho_act_net_fluxes]),
("rho_inact_net_fluxes", [float(v) for v in rho_inact_net_fluxes]),
("x_tens", [float(strain_inhibition) for _ in local_strains])]
# for d in data:
# logging.log(level=99, msg="{}: {}".format(d[0], d[1]))
writer.save_int_step(data)
for ni in range(16):
old_coord = poly[ni]
new_verts[ni][0] = old_coord[0] + dt * sum_forces_x[ni] / vertex_eta
new_verts[ni][1] = old_coord[1] + dt * sum_forces_y[ni] / vertex_eta
# for ix in focus_verts:
# logging.log(level=DYNAMICS_INFO, msg="delta.poly[{}]: {}"
# .format(ix, (new_verts[0] - poly[0]) / dt)
# )
# logging.log(level=DYNAMICS_INFO,
# msg="expected Delta poly 0 ({}): {}"
# .format(ix, dt * sum_forces[0] / vertex_eta)
# )
verts_before_ve = copy.deepcopy(new_verts)
# calculate volume exclusion effects
num_bisection_iterations = 10
max_movement_mag = dt * const_protrusive / vertex_eta
for other_ci in range(num_cells):
if other_ci != cell_ix:
# logging.log(level=VOL_EX_INFO, msg="testing poly: {}".format(
# other_ci))
# logging.log(level=VOL_EX_INFO,
# msg="coords: {}".format(all_cells_verts[other_ci]))
# logging.log(level=VOL_EX_INFO,
# msg="max movement mag: {}".format(max_movement_mag))
are_new_nodes_inside_other_cell = \
geometry.are_points_inside_polygon(
new_verts, all_cells_verts[other_ci]
)
# logging.log(level=VOL_EX_INFO, msg="in poly: {}".format(
# [i for (i, x) in
# enumerate(are_new_nodes_inside_other_cell) if x])
# )
for ni in range(16):
if are_new_nodes_inside_other_cell[ni]:
# logging.log(level=VOL_EX_INFO,
# msg="fixing vertex {} violation (current: {})".format(
# ni, new_verts[ni]))
new_verts[ni] = enforce_volume_exclusion_for_vertex(
poly[ni],
new_verts[ni],
uivs[ni],
all_cells_verts[other_ci],
num_bisection_iterations,
max_movement_mag,
)
verts_after_ve = copy.deepcopy(new_verts)
for ni in range(16):
new_coord = new_verts[ni]
old_coord = poly[ni]
delta_x[ni] = (new_coord[0] - old_coord[0]) / dt
delta_y[ni] = (new_coord[1] - old_coord[1]) / dt
for ni in range(16):
# finish assigning chemistry variables
delta_rac_activated[ni] = kgtps_rac[ni] * rac_inacts[ni]
delta_rac_inactivated[ni] = kdgtps_rac[ni] * rac_acts[ni]
delta_rac_on = k_mem_on_vertex * rac_cyto
delta_rac_off = k_mem_off * rac_inacts[ni]
delta_rac_cytosol_to_membrane[ni] = delta_rac_on - delta_rac_off
delta_rho_activated[ni] = kgtps_rho[ni] * rho_inacts[ni]
delta_rho_inactivated[ni] = kdgtps_rho[ni] * rho_acts[ni]
delta_rho_on = k_mem_on_vertex * rho_cyto
delta_rho_off = k_mem_off * rho_inacts[ni]
delta_rho_cytosol_to_membrane[ni] = delta_rho_on - delta_rho_off
# set up ode array
ode_array = np.empty(num_phase_vars * 16)
for i in range(16):
ode_array[i] = (delta_rac_activated[i] - delta_rac_inactivated[i] +
rac_act_net_fluxes[i])
ode_array[i + 16] = (delta_rac_inactivated[i] -
delta_rac_activated[i] + rac_inact_net_fluxes[i] +
delta_rac_cytosol_to_membrane[i])
ode_array[i +
2 * 16] = (delta_rho_activated[i] -
delta_rho_inactivated[i] + rho_act_net_fluxes[i])
ode_array[i +
3 * 16] = (delta_rho_inactivated[i] -
delta_rho_activated[i] + rho_inact_net_fluxes[i] +
delta_rho_cytosol_to_membrane[i])
ode_array[i + 4 * 16] = delta_x[i]
ode_array[i + 5 * 16] = delta_y[i]
return ode_array, sum_forces, edge_forces_plus, edge_forces_minus, \
rgtp_forces, cyto_forces, verts_before_ve, verts_after_ve
def initialize_cell(
self,
close_point_smoothness_factors,
x_cils,
x_coas,
):
verts = self.curr_verts
self.curr_state[:, [parameters.x_ix, parameters.y_ix]] = verts
self.curr_state[:, parameters.edge_lengths_ix] = \
self.rest_edge_len * np.ones(16)
if self.cell_ix == 0:
self.set_rgtp_distrib(
self.init_rac,
self.init_rho,
)
else:
self.set_rgtp_distrib(
self.init_rho,
self.init_rac,
)
rac_acts = self.curr_state[:, parameters.rac_act_ix]
rho_acts = self.curr_state[:, parameters.rho_act_ix]
self.curr_state[:, parameters.old_x_coa_ix] = x_coas
self.curr_state[:, parameters.old_x_cil_ix] = x_cils
sum_forces, edge_forces_plus, edge_forces_minus, uevs, rgtpase_forces, \
cyto_forces, \
edge_strains, local_strains, uivs = \
mechanics.calculate_forces(
verts,
rac_acts,
rho_acts,
self.rest_edge_len,
self.stiffness_edge,
self.halfmax_vertex_rgtp,
self.const_protrusive,
self.const_retractive,
self.rest_area,
self.stiffness_cyto,
)
self.curr_state[:, parameters.local_strains_ix] = local_strains
edgeplus_lengths = geometry.calculate_edgeplus_lengths(verts)
avg_edge_lengths = geometry.calculate_average_edge_length_around_nodes(
edgeplus_lengths)
conc_rac_acts = chemistry.calc_concs(rac_acts, avg_edge_lengths)
conc_rho_acts = chemistry.calc_concs(rho_acts, avg_edge_lengths)
self.curr_state[:, parameters.rac_rands_ix] = self.rac_rands
kgtp_racs = chemistry.calculate_kgtp_rac(
conc_rac_acts,
self.halfmax_vertex_rgtp_conc,
self.kgtp_rac,
self.kgtp_rac_auto,
x_coas,
self.rac_rands,
x_cils,
close_point_smoothness_factors,
)
self.curr_state[:, parameters.kgtp_rac_ix] = kgtp_racs
kgtp_rhos = chemistry.calculate_kgtp_rho(
conc_rho_acts,
x_cils,
self.halfmax_vertex_rgtp_conc,
self.kgtp_rho,
self.kgtp_rho_auto,
)
self.curr_state[:, parameters.kgtp_rho_ix] = kgtp_rhos
self.curr_state[:, parameters.kdgtp_rac_ix] = \
chemistry.calculate_kdgtp_rac(
conc_rho_acts,
self.halfmax_vertex_rgtp_conc,
self.kdgtp_rac,
self.kdgtp_rho_on_rac,
x_cils,
self.halfmax_tension_inhib,
self.tension_inhib,
np.array([ls if ls > 0 else 0.0 for ls in local_strains]),
)
self.curr_state[:, parameters.kdgtp_rho_ix] = \
chemistry.calculate_kdgtp_rho(
conc_rac_acts,
self.halfmax_vertex_rgtp_conc,
self.kdgtp_rho,
self.kdgtp_rac_on_rho,
)
# update mechanics parameters
self.curr_state[:, [parameters.sum_forces_x_ix,
parameters.sum_forces_y_ix]] \
= sum_forces
self.curr_state[:, [parameters.edge_forces_plus_x_ix,
parameters.edge_forces_plus_y_ix]] = \
edge_forces_plus
self.curr_state[:, [parameters.edge_forces_minus_x_ix,
parameters.edge_forces_minus_y_ix]] = \
edge_forces_minus
self.curr_state[:, [parameters.rgtp_forces_x_ix,
parameters.rgtp_forces_y_ix]] \
= rgtpase_forces
self.curr_state[:, [parameters.cyto_forces_x_ix,
parameters.cyto_forces_y_ix]] = \
cyto_forces
self.curr_state[:, [parameters.uiv_x_ix, parameters.uiv_y_ix]] = uivs
self.curr_verts = verts
def cell_dynamics(state_array, t0, state_parameters, this_cell_index, num_nodes, num_nodal_phase_vars, num_ode_cellwide_phase_vars, nodal_rac_membrane_active_index, length_edge_resting, nodal_rac_membrane_inactive_index, nodal_rho_membrane_active_index, nodal_rho_membrane_inactive_index, nodal_x_index, nodal_y_index, kgtp_rac_baseline, kdgtp_rac_baseline, kgtp_rho_baseline, kdgtp_rho_baseline, kgtp_rac_autoact_baseline, kgtp_rho_autoact_baseline, kdgtp_rho_mediated_rac_inhib_baseline, kdgtp_rac_mediated_rho_inhib_baseline, kgdi_rac, kdgdi_rac, kgdi_rho, kdgdi_rho, threshold_rac_autoact, threshold_rho_autoact, threshold_rho_mediated_rac_inhib, threshold_rac_mediated_rho_inhib, exponent_rac_autoact, exponent_rho_autoact, exponent_rho_mediated_rac_inhib, exponent_rac_mediated_rho_inhib, diffusion_const_active, diffusion_const_inactive, nodal_intercellular_contact_factor_magnitudes_index, nodal_migr_bdry_contact_index, space_at_node_factor_rac, space_at_node_factor_rho, eta, num_cells, all_cells_node_coords, intercellular_squared_dist_array, stiffness_edge, force_rac_exp, force_rac_threshold, force_rac_max_mag, force_rho_exp, force_rho_threshold, force_rho_max_mag, area_resting, stiffness_cytoplasmic, transduced_coa_signals, space_physical_bdry_polygon, exists_space_physical_bdry_polygon, are_nodes_inside_other_cells, close_point_on_other_cells_to_each_node_exists, intercellular_contact_factors, tension_mediated_rac_inhibition_exponent, tension_mediated_rac_inhibition_multiplier, tension_mediated_rac_hill_exponent, tension_mediated_rac_inhibition_half_strain, tension_fn_type, external_gradient_on_nodes, intercellular_contact_factor_magnitudes):
nodal_phase_vars = state_array
rac_mem_active_start_index = nodal_rac_membrane_active_index*num_nodes
rac_mem_active_end_index = rac_mem_active_start_index + num_nodes
rac_membrane_active = nodal_phase_vars[rac_mem_active_start_index:rac_mem_active_end_index]
rac_mem_inactive_start_index = nodal_rac_membrane_inactive_index*num_nodes
rac_mem_inactive_end_index = rac_mem_inactive_start_index + num_nodes
rac_membrane_inactive = nodal_phase_vars[rac_mem_inactive_start_index:rac_mem_inactive_end_index]
rho_mem_active_start_index = nodal_rho_membrane_active_index*num_nodes
rho_mem_active_end_index = rho_mem_active_start_index + num_nodes
rho_membrane_active = nodal_phase_vars[rho_mem_active_start_index:rho_mem_active_end_index]
rho_mem_inactive_start_index = nodal_rho_membrane_inactive_index*num_nodes
rho_mem_inactive_end_index = rho_mem_inactive_start_index + num_nodes
rho_membrane_inactive = nodal_phase_vars[rho_mem_inactive_start_index:rho_mem_inactive_end_index]
nodal_x_start_index = nodal_x_index*num_nodes
nodal_x_end_index = nodal_x_start_index + num_nodes
nodal_x = nodal_phase_vars[nodal_x_start_index:nodal_x_end_index]
nodal_y_start_index = nodal_y_index*num_nodes
nodal_y_end_index = nodal_y_start_index + num_nodes
nodal_y = nodal_phase_vars[nodal_y_start_index:nodal_y_end_index]
node_coords = general_utilities.make_node_coords_array_given_xs_and_ys(num_nodes, nodal_x, nodal_y)
rac_cytosolic_gdi_bound = 1 - calculate_sum(num_nodes, rac_membrane_active) - calculate_sum(num_nodes, rac_membrane_inactive)
rho_cytosolic_gdi_bound = 1 - calculate_sum(num_nodes, rho_membrane_active) - calculate_sum(num_nodes, rho_membrane_inactive)
# calculate forces
F, EFplus, EFminus, F_rgtpase, F_cytoplasmic, local_strains, unit_inside_pointing_vectors = mechanics.calculate_forces(num_nodes, node_coords, rac_membrane_active, rho_membrane_active, length_edge_resting, stiffness_edge, force_rac_exp, force_rac_threshold, force_rac_max_mag, force_rho_exp, force_rho_threshold, force_rho_max_mag, area_resting, stiffness_cytoplasmic)
F_x = F[:, 0]
F_y = F[:, 1]
migr_bdry_contact_factors = state_parameters[nodal_migr_bdry_contact_index]
only_tensile_local_strains = np.zeros_like(local_strains)
for i in range(num_nodes):
local_strain = local_strains[i]
if local_strain > 0:
only_tensile_local_strains[i] = local_strain
kgtps_rac = chemistry.calculate_kgtp_rac(num_nodes, rac_membrane_active, migr_bdry_contact_factors, exponent_rac_autoact, threshold_rac_autoact, kgtp_rac_baseline, kgtp_rac_autoact_baseline, transduced_coa_signals, external_gradient_on_nodes)
kdgtps_rac = chemistry.calculate_kdgtp_rac(num_nodes, rho_membrane_active, exponent_rho_mediated_rac_inhib, threshold_rho_mediated_rac_inhib, kdgtp_rac_baseline, kdgtp_rho_mediated_rac_inhib_baseline, intercellular_contact_factors, migr_bdry_contact_factors, tension_mediated_rac_inhibition_exponent, tension_mediated_rac_inhibition_multiplier, tension_mediated_rac_hill_exponent, tension_mediated_rac_inhibition_half_strain, local_strains, tension_fn_type)
kdgdis_rac = kdgdi_rac*np.ones(num_nodes, dtype=np.float64)
kgtps_rho = chemistry.calculate_kgtp_rho(num_nodes, rho_membrane_active, intercellular_contact_factors, migr_bdry_contact_factors, exponent_rho_autoact, threshold_rho_autoact, kgtp_rho_baseline, kgtp_rho_autoact_baseline)
kdgtps_rho = chemistry.calculate_kdgtp_rho(num_nodes, rac_membrane_active, exponent_rac_mediated_rho_inhib, threshold_rac_mediated_rho_inhib, kdgtp_rho_baseline, kdgtp_rac_mediated_rho_inhib_baseline)
kdgdis_rho = kdgdi_rho*np.ones(num_nodes, dtype=np.float64)
edgeplus_lengths = geometry.calculate_edgeplus_lengths(num_nodes, node_coords)
diffusion_rac_membrane_active = chemistry.calculate_diffusion(num_nodes, rac_membrane_active, diffusion_const_active, edgeplus_lengths)
diffusion_rac_membrane_inactive = chemistry.calculate_diffusion(num_nodes, rac_membrane_inactive, diffusion_const_inactive, edgeplus_lengths)
diffusion_rho_membrane_active = chemistry.calculate_diffusion(num_nodes, rho_membrane_active, diffusion_const_active, edgeplus_lengths)
diffusion_rho_membrane_inactive = chemistry.calculate_diffusion(num_nodes, rho_membrane_inactive, diffusion_const_active, edgeplus_lengths)
delta_rac_activated = np.zeros(num_nodes, dtype=np.float64)
delta_rac_inactivated = np.zeros(num_nodes, dtype=np.float64)
delta_rac_cytosol_to_membrane = np.zeros(num_nodes, dtype=np.float64)
delta_rho_activated = np.zeros(num_nodes, dtype=np.float64)
delta_rho_inactivated = np.zeros(num_nodes, dtype=np.float64)
delta_rho_cytosol_to_membrane = np.zeros(num_nodes, dtype=np.float64)
delta_nodal_x = np.zeros(num_nodes, dtype=np.float64)
delta_nodal_y = np.zeros(num_nodes, dtype=np.float64)
new_node_coords = np.zeros((num_nodes, 2), dtype=np.float64)
new_coord = np.zeros(2, dtype=np.float64)
old_coord = np.zeros(2, dtype=np.float64)
for ni in range(num_nodes):
old_coord = node_coords[ni]
new_node_coords[ni][0] = old_coord[0] + F_x[ni]/eta
new_node_coords[ni][1] = old_coord[1] + F_y[ni]/eta
# calculate volume exclusion effects
num_bisection_iterations = 2
max_movement_mag = (force_rac_max_mag/eta)
success_condition_stay_out = 0
success_condition_stay_in = 1
are_new_nodes_inside_other_cell = np.zeros(num_nodes, dtype=np.int64)
for other_ci in range(num_cells):
if other_ci != this_cell_index:
are_new_nodes_inside_other_cell = geometry.are_points_inside_polygon(num_nodes, new_node_coords, num_nodes, all_cells_node_coords[other_ci])
for ni in range(num_nodes):
if are_new_nodes_inside_other_cell[ni] != success_condition_stay_out:
new_node_coords[ni] = calculate_volume_exclusion_effects(node_coords[ni], new_node_coords[ni], unit_inside_pointing_vectors[ni], all_cells_node_coords[other_ci], num_bisection_iterations, max_movement_mag, success_condition_stay_out)
if exists_space_physical_bdry_polygon == 1:
are_new_nodes_inside_space_physical_bdry_polygon = geometry.are_points_inside_polygon(num_nodes, new_node_coords, space_physical_bdry_polygon.shape[0], space_physical_bdry_polygon)
for ni in range(num_nodes):
if are_new_nodes_inside_space_physical_bdry_polygon[ni] != success_condition_stay_in:
new_node_coords[ni] = calculate_volume_exclusion_effects(node_coords[ni], new_node_coords[ni], unit_inside_pointing_vectors[ni], space_physical_bdry_polygon, num_bisection_iterations, max_movement_mag, success_condition_stay_in)
for ni in range(num_nodes):
new_coord = new_node_coords[ni]
old_coord = node_coords[ni]
delta_nodal_x[ni] = new_coord[0] - old_coord[0]
delta_nodal_y[ni] = new_coord[1] - old_coord[1]
for ni in range(num_nodes):
# finish assigning chemistry variables
delta_rac_activated[ni] = kgtps_rac[ni]*rac_membrane_inactive[ni]
delta_rac_inactivated[ni] = kdgtps_rac[ni]*rac_membrane_active[ni]
delta_rac_on = kdgdis_rac[ni]*rac_cytosolic_gdi_bound
delta_rac_off = kgdi_rac*rac_membrane_inactive[ni]
delta_rac_cytosol_to_membrane[ni] = delta_rac_on - delta_rac_off
delta_rho_activated[ni] = kgtps_rho[ni]*rho_membrane_inactive[ni]
delta_rho_inactivated[ni] = kdgtps_rho[ni]*rho_membrane_active[ni]
delta_rho_on = kdgdis_rho[ni]*rho_cytosolic_gdi_bound
delta_rho_off = kgdi_rho*rho_membrane_inactive[ni]
delta_rho_cytosol_to_membrane[ni] = delta_rho_on - delta_rho_off
# set up ode array
ode_array = np.empty(num_nodal_phase_vars*num_nodes)
for i in range(num_nodes):
ode_array[i] = delta_rac_activated[i] - delta_rac_inactivated[i] + diffusion_rac_membrane_active[i]
ode_array[i + num_nodes] = delta_rac_inactivated[i] - delta_rac_activated[i] + diffusion_rac_membrane_inactive[i] + delta_rac_cytosol_to_membrane[i]
ode_array[i + 2*num_nodes] = delta_rho_activated[i] - delta_rho_inactivated[i] + diffusion_rho_membrane_active[i]
ode_array[i + 3*num_nodes] = delta_rho_inactivated[i] - delta_rho_activated[i] + diffusion_rho_membrane_inactive[i] + delta_rho_cytosol_to_membrane[i]
ode_array[i + 4*num_nodes] = delta_nodal_x[i]
ode_array[i + 5*num_nodes] = delta_nodal_y[i]
return ode_array