mpacts.contact.models.collision.cellmigration. cellmigration_matrix

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

import mpacts.contact.models.collision.cellmigration.cellmigration_matrix
#or assign it to a shorter name
import mpacts.contact.models.collision.cellmigration.cellmigration_matrix as cel

HaptotaxisJKR

Description: Normal contact model which pulls cells within a range together (haptotaxis). Uses JKR contact potential and assembles virial stress. Warning: Contact dectection must be adjusted to take into account the ‘range’ as defined in HaptotaxisForce.h! Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

HaptotaxisJKR (Sphere Sphere)

Normal contact model which pulls cells within a range together (haptotaxis). Uses JKR contact potential and assembles virial stress. Warning: Contact dectection must be adjusted to take into account the ‘range’ as defined in HaptotaxisForce.h!

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E1 (kg . m^-1 . s^-2) — Young modulus material 1.
    • E2 (kg . m^-1 . s^-2) — Young modulus material 2.
    • force — Haptotaxic force. Positive force is attractive interaction!
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu1 (1) — Poisson ratio material 1.
    • nu2 (1) — Poisson ratio material 2.
    • p_connect — Probability of a connection being formed (in one timestep)
    • p_release — Probability of a connection being broken (in one timestep)
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
    • range — Range of haptotaxic interaction, defined from sphere surface to surface
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • attrConst1 (kg . s^-2) (default value = 0) — Adhesion energy of material 1
    • attrConst2 (kg . s^-2) (default value = 0) — Adhesion energy of material 2
    • attrConst (kg . s^-2) (default value = -1) — Combined adhesion energy. Always over-rules attrConst1 and attrConst2, even if given as arrays!
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereSingleValue_Property  <double >
  ↓
N_JKRHaptotaxisForceN_T_AreaWeightedResistanceAssembleForcesAssemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContacts

HaptotaxisRandomWalkJKR

Description: Normal contact model which pulls cells within a range together (haptotaxis) and tangential random walking force. Uses JKR contact potential and assembles virial stress. Warning: Contact dectection must be adjusted to take into account the ‘range’ as defined in HaptotaxisForce.h! Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

HaptotaxisRandomWalkJKR (Sphere Sphere)

Normal contact model which pulls cells within a range together (haptotaxis) and tangential random walking force. Uses JKR contact potential and assembles virial stress. Warning: Contact dectection must be adjusted to take into account the ‘range’ as defined in HaptotaxisForce.h!

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E1 (kg . m^-1 . s^-2) — Young modulus material 1.
    • E2 (kg . m^-1 . s^-2) — Young modulus material 2.
    • force — Haptotaxic force. Positive force is attractive interaction!
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu1 (1) — Poisson ratio material 1.
    • nu2 (1) — Poisson ratio material 2.
    • p_connect — Probability of a connection being formed (in one timestep)
    • p_release — Probability of a connection being broken (in one timestep)
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
    • range — Range of haptotaxic interaction, defined from sphere surface to surface
    • rotation — Amount of rotation with which the direction is changed at each time step.
    • traction — Tangential walking force applied to achieve relative motion (e.g. cell migration).
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • attrConst1 (kg . s^-2) (default value = 0) — Adhesion energy of material 1
    • attrConst2 (kg . s^-2) (default value = 0) — Adhesion energy of material 2
    • attrConst (kg . s^-2) (default value = -1) — Combined adhesion energy. Always over-rules attrConst1 and attrConst2, even if given as arrays!
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereSingleValue_Property  <double >
  ↓
N_JKRHaptotaxisForceT_RandomWalkN_T_AreaWeightedResistanceAssembleForcesAssemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContacts

RandomWalkJKR

Description: Tangential contact model which makes cells randomly walk another particle / cell. Uses JKR contact potential and assembles virial stress. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

RandomWalkJKR (Sphere Sphere)

Tangential contact model which makes cells randomly walk another particle / cell. Uses JKR contact potential and assembles virial stress.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E1 (kg . m^-1 . s^-2) — Young modulus material 1.
    • E2 (kg . m^-1 . s^-2) — Young modulus material 2.
    • gamma_normal (kg . s^-1 . m^-2) — Normal friction coefficient (Pa*s/m)
    • gamma_tangential (kg . s^-1 . m^-2) — Tangential friction coefficient (Pa*s/m)
    • nu1 (1) — Poisson ratio material 1.
    • nu2 (1) — Poisson ratio material 2.
    • pc1 — The first particle container in the binary contact detection.
    • pc2 — The second particle container in the binary contact detection. If contact detection within the same particle container is desired, and it is applicable for the contactmodel, pass the same pc to both pc1 and pc2.
    • rotation — Amount of rotation with which the direction is changed at each time step.
    • traction — Tangential walking force applied to achieve relative motion (e.g. cell migration).
  • Optional keywords:
    • _contactmatrixdatatype (default value = 1) — Identifier that signals that this chain element’s containing contact model is a friction matrix type. Only change this if you really know what you are doing!
    • attrConst1 (kg . s^-2) (default value = 0) — Adhesion energy of material 1
    • attrConst2 (kg . s^-2) (default value = 0) — Adhesion energy of material 2
    • attrConst (kg . s^-2) (default value = -1) — Combined adhesion energy. Always over-rules attrConst1 and attrConst2, even if given as arrays!
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).

This contact model is composed out of following pieces (click on the chain elements to get more information):

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereSingleValue_Property  <double >
  ↓
N_JKRT_RandomWalkN_T_AreaWeightedResistanceAssembleForcesAssemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContacts