mpacts.commands.misc. lamellipodiumfront

In order to be able to use this module import it like this:

import mpacts.commands.misc.lamellipodiumfront
#or assign it to a shorter name
import mpacts.commands.misc.lamellipodiumfront as lam

CellFrontCommand

class mpacts.commands.misc.lamellipodiumfront.CellFrontCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Computes a cell front based on its bias direction and a distance fron the cell’s centre. A given average traction array will be distributed to those triangles in the cell front
Default location: ‘loop_cmds/pre_contact_cmds’
  • Required keywords:
    • pc — Particle container on which the command is applied
    • traction_cell — Array keeping the average traction per cell. The actual local traction will be traction * contact_area / front_area >= average_traction!
    • traction_triangle — Scalar array keeping the active traction value per triangle
  • Optional keywords:
    • bias_angle (default value = 1.5707963267948966) — Maximal angle between bias direction and the triangle’s relative position to the center to be in the cell’s front.
    • dist_from_center (default value = 0) — SIGNED (so can be negative!) distance from the center of the cell in the direction of cell’s bias to be considered in the cells front.
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, traction_triangle, traction_cell, [gate, predicate, bias_angle, dist_from_center]
CellFrontCommand(name, parent, **kwargs)

CellFrontTipCommand

class mpacts.commands.misc.lamellipodiumfront.CellFrontTipCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Computes a cell front based on its bias direction and the distance from the cell’s tip. A given average traction array will be distributed to those triangles in the cell front
Default location: ‘loop_cmds/pre_contact_cmds’
  • Required keywords:
    • pc — Particle container on which the command is applied
    • traction_cell — Array keeping the average traction per cell. The actual local traction will be traction * contact_area / front_area >= average_traction!
    • traction_triangle — Scalar array keeping the active traction value per triangle
  • Optional keywords:
    • dist_from_front (default value = 0) — SIGNED (so can be negative!) distance from the front of the cell in the direction of cell’s bias to be considered in the cells front.
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, traction_triangle, traction_cell, [gate, predicate, dist_from_front]
CellFrontTipCommand(name, parent, **kwargs)

CellFrontTipCommandM

class mpacts.commands.misc.lamellipodiumfront.CellFrontTipCommandM

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Computes a cell bottom based on its bias direction and the distance from the cell’s tip. A given average traction array will be distributed to those triangles in the cell bottom
Default location: ‘loop_cmds/pre_contact_cmds’
  • Required keywords:
    • pc — Particle container on which the command is applied
    • traction_cell — Array keeping the average traction per cell. The actual local traction will be traction * contact_area / front_area >= average_traction!
    • traction_triangle — Scalar array keeping the active traction value per triangle
  • Optional keywords:
    • dist_from_front (default value = 0) — SIGNED (so can be negative!) distance from the front of the cell in the direction of cell’s bias to be considered in the cells front.
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
    • traction_Factor (default value = 0) — Scalar, indicating the difference in traction between front and back of cell
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, traction_triangle, traction_cell, [gate, predicate, dist_from_front, traction_Factor]
CellFrontTipCommandM(name, parent, **kwargs)

InitFilopodiaCommand

class mpacts.commands.misc.lamellipodiumfront.InitFilopodiaCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Randomly initializes a set of ‘controlPoints’ (containing an xBF array) that act as filopodia and can e.g. exert force on the parent particle. Usually needs a predicate!
Default location: ‘loop_cmds/pre_body_force_cmds’
  • Required keywords:
    • direction — Array with a direction vector of the parent particle container (i.e. the cell).
    • max_angle — maximal angle that a new filopodium can make with respect to the polarization vector of the cell.
    • mean_distance — mean distance from the cell center to which the filopodium will be projected.
    • pc — Particle container on which the command is applied
    • std_distance — standard deviation on the distance from the cell center that the filopodium will be projected to.
  • Optional keywords:
    • ext0 (default value = 1) — Initial extension of new filopodia. Default=1.
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • min_distance (default value = 0) — optional minimum distance that the filopodium can ever be projected, regardless of the random number. Default=0.
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
    • restrict_to_plane (default value = 0 0 0) — If a plane normal is given, the command will project its direction in the plane.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, mean_distance, std_distance, max_angle, direction, [gate, predicate, min_distance, ext0, restrict_to_plane]
InitFilopodiaCommand(name, parent, **kwargs)

InitFilopodiaDeformableCommand

class mpacts.commands.misc.lamellipodiumfront.InitFilopodiaDeformableCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Randomly initializes filopodia positions as function of a base cell membrane position. Usually needs a predicate!
Default location: ‘loop_cmds/body_force_cmds’
  • Required keywords:
    • max_angle — maximal angle that a new filopodium can make with respect to the polarization vector of the cell.
    • mean_distance — mean distance from the cell membrane node to which the filopodium will be projected.
    • pc — Particle container on which the command is applied
    • std_distance — standard deviation on the distance from the cell membrane node that the filopodium will be projected to.
  • Optional keywords:
    • ext0 (default value = 1) — Initial extension of new filopodia. Default=1.
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • min_distance (default value = 0) — optional minimum distance that the filopodium can ever be projected, regardless of the random number. Default=0.
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
    • restrict_to_plane (default value = 0 0 0) — If a plane normal is given, the command will project its direction in the plane.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, mean_distance, std_distance, max_angle, [gate, predicate, min_distance, ext0, restrict_to_plane]
InitFilopodiaDeformableCommand(name, parent, **kwargs)

LamellipodiumFrontCommand

class mpacts.commands.misc.lamellipodiumfront.LamellipodiumFrontCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Command to set the Lamellipodium’s surface area for a wallking deformable cell; sets the given contact area array to -1 for non-motile triangles.
Default location: ‘loop_cmds/pre_contact_cmds’
  • Required keywords:
    • contact_area — Copied ‘contact_area’ array for subsequent contact loop.
    • lower_contact_fraction — Fraction of contact_area/triangle_area that defines a triangle to be in ‘sufficient partial contact’.
    • pc — Particle container on which the command is applied
    • upper_contact_fraction — Fraction of contact_area/triangle_area that defines a triangle to be in ‘basically full contact’.
  • Optional keywords:
    • bias_angle (default value = 1.5707963267948966) — Maximal angle between bias direction and triangle outward normal to justify adding motion force (in radian).
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, upper_contact_fraction, lower_contact_fraction, contact_area, [gate, predicate, bias_angle]
LamellipodiumFrontCommand(name, parent, **kwargs)

MeanContactAreaCommand

class mpacts.commands.misc.lamellipodiumfront.MeanContactAreaCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Computes a mean contact area based on the normals and areas of triangles in contact
Default location: ‘loop_cmds/pre_body_force_cmds’
  • Required keywords:
    • Mean_Plane — Array with a mean plane vector
    • pc — Particle container on which the command is applied
  • Optional keywords:
    • Minimal_area (default value = 0) — Minimal contact area of triangles which are included
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, Mean_Plane, [gate, predicate, Minimal_area]
MeanContactAreaCommand(name, parent, **kwargs)

PeripheryCommand

class mpacts.commands.misc.lamellipodiumfront.PeripheryCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Computes tractions in the cell periphery from a “maximum” traction and a scaleing array.
Default location: ‘loop_cmds/pre_contact_cmds’
  • Required keywords:
    • pc — Particle container on which the command is applied
    • traction_cell — Array keeping the ‘maximum’ traction per triangle. The actual local traction will be: traction * contact_area / front_area >= maximum_traction
    • traction_scale — Array with which tractions are scaled. In principle it should be between 0 and 1, but we ensure the limits.
    • traction_triangle — Scalar array keeping the active traction value per triangle
  • Optional keywords:
    • dist_from_center (default value = 0) — Distance from the center of the cell to be considered in the cells front.
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • minimal_traction_scale (default value = 0) — Minimal value with which tractions will be scaled, default: 0.
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
    • restrict_distance (default value = 1) — Distance from plane that still allows for tractions. Default: 1., i.e. everything.
    • restrict_plane_normal (default value = 0 0 0) — Plane normal to which the cell-center will be projected and the peripherial tractions will be restricted; if not a unit-vector, it will be disregarded (default).
    • restrict_plane_point (default value = 0 0 0) — Point on plane to which the peripherial tractions will be restricted (default: 0,0,0)
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, traction_triangle, traction_cell, traction_scale, [gate, predicate, dist_from_center, restrict_plane_normal, restrict_plane_point, restrict_distance, minimal_traction_scale]
PeripheryCommand(name, parent, **kwargs)

SPHFocalAdhesionCommand

class mpacts.commands.misc.lamellipodiumfront.SPHFocalAdhesionCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Generate and remove adhesion for cell-SPH simulations
Default location: ‘loop_cmds/pre_body_force_cmds’
  • Required keywords:
    • F_break — Force at which adhesion breaks (will be scaled by adhesion maturation parameter)
    • Pb — Probaility of binding (forming FA when free)
    • Pd — Probaility of decoupling FA
    • dt — sim time step
    • gamma_exp — decay constant for focal adhesion disassembly at low forces
    • l_init — init length adhesion
    • max_age — maximum lifetime protrusion
    • min_age — minimum lifetime protrusion
    • pc — Particle container on which the command is applied
    • th_ss — threshold supportSum for adhesion breaking
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, Pb, Pd, dt, l_init, th_ss, max_age, min_age, F_break, gamma_exp, [gate, predicate]
SPHFocalAdhesionCommand(name, parent, **kwargs)

SPHFocalAdhesionDeflectionCommand

class mpacts.commands.misc.lamellipodiumfront.SPHFocalAdhesionDeflectionCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Generate and remove adhesion for cell-SPH simulations
Default location: ‘loop_cmds/pre_body_force_cmds’
  • Required keywords:
    • F_break — Force at which adhesion breaks (will be scaled by adhesion maturation parameter)
    • P_0 — Probability of decoupling FA at zero force
    • P_min — Minimal probability of decoupling FA
    • Pb — Probaility of binding (forming FA when free)
    • dt — sim time step
    • gamma_exp — decay constant for focal adhesion disassembly at low forces
    • l_init — init length adhesion
    • max_age — maximum lifetime protrusion
    • min_age — minimum lifetime protrusion
    • pc — Particle container on which the command is applied
    • th_ss — threshold supportSum for adhesion breaking
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, Pb, P_min, P_0, dt, l_init, th_ss, max_age, min_age, F_break, gamma_exp, [gate, predicate]
SPHFocalAdhesionDeflectionCommand(name, parent, **kwargs)

SPHFocalAdhesionDeflectionNoBreakingCommand

class mpacts.commands.misc.lamellipodiumfront.SPHFocalAdhesionDeflectionNoBreakingCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Generate and remove adhesion for cell-SPH simulations
Default location: ‘loop_cmds/pre_body_force_cmds’
  • Required keywords:
    • P_0 — Probability of decoupling FA at zero force
    • P_min — Minimal probability of decoupling FA
    • Pb — Probaility of binding (forming FA when free)
    • dt — sim time step
    • gamma_exp — decay constant for focal adhesion disassembly at low forces
    • l_init — init length adhesion
    • max_age — maximum lifetime protrusion
    • min_age — minimum lifetime protrusion
    • pc — Particle container on which the command is applied
    • th_ss — threshold supportSum for adhesion breaking
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, Pb, P_min, P_0, dt, l_init, th_ss, max_age, min_age, gamma_exp, [gate, predicate]
SPHFocalAdhesionDeflectionNoBreakingCommand(name, parent, **kwargs)

SPHFocalAdhesionForceCommand

class mpacts.commands.misc.lamellipodiumfront.SPHFocalAdhesionForceCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Apply adhesion force for cell-SPH simulatios
Default location: ‘loop_cmds/pre_body_force_cmds’
  • Required keywords:
    • k_ad — adhesion spring constant
    • l_init — init length adhesion
    • pc — Particle container on which the command is applied
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, l_init, k_ad, [gate, predicate]
SPHFocalAdhesionForceCommand(name, parent, **kwargs)

SPHProtrusionCommand

class mpacts.commands.misc.lamellipodiumfront.SPHProtrusionCommand

Bases: mpacts.core.command.Command, mpacts.core.baseobject.BaseObject

Generate protrusions for cell-SPH simulations
Default location: ‘loop_cmds/pre_body_force_cmds’
  • Required keywords:
    • P_prot — Probaility of binding (forming FA when free)
    • dt — sim time step
    • pc — Particle container on which the command is applied
  • Optional keywords:
    • gate (default value = ET::ChildProperty const*) — Can decide to (temporarily) not execute the command in a CommandList. (Default is ExecuteAlways)
    • predicate (default value = None) — Predicate that will decide whether this command is executed for a specific particle, when absent the command is executed for every particle.
object __init__(tuple args, dict kwds) :
args: name, parent kwds: pc, P_prot, dt, [gate, predicate]
SPHProtrusionCommand(name, parent, **kwargs)