mpacts.contact.models.collision. celldivision

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

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

BuddingJKRMatrix

Description: Budding (e.g. budding yeast) cells that - if not dividing - interact with a JKR adhesive/repulsive contact force Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

BuddingJKRMatrix (Sphere Sphere)

Budding (e.g. budding yeast) cells that - if not dividing - interact with a JKR adhesive/repulsive contact force

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.
    • division_force — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time — time it takes for the cytokinesis to complete
    • divstiffatt — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • 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.
    • state_bud — State value of the bud.
    • state_mother — State value of the mother cell.
  • 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_SphereN_BuddingSingleValue_Property  <double >
  ↓
N_JKRN_T_AreaWeightedResistanceN_DividingResistanceAssembleForcesAssemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContactsFeedbackDividing

BuddingVarJKRMatrix

Description: Budding (e.g. budding yeast) cells that - if not dividing - interact with a JKR adhesive/repulsive contact force. Adhesion energy, stiffness, and contact friction vary with an array Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

BuddingVarJKRMatrix (Sphere Sphere)

Budding (e.g. budding yeast) cells that - if not dividing - interact with a JKR adhesive/repulsive contact force. Adhesion energy, stiffness, and contact friction vary with an array

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E1 — Young modulus material 1.
    • E2 — Young modulus material 2.
    • division_force — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time — time it takes for the cytokinesis to complete
    • divstiffatt — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • 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.
    • state_bud — State value of the bud.
    • state_mother — State value of the mother cell.
  • 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 (default value = None) — Adhesion energy of material 1
    • attrConst2 (default value = None) — 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_SphereN_BuddingArrayValue_Property  <double >
  ↓
N_JKRN_T_AreaWeightedResistanceN_DividingResistanceAssembleForcesAssemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContactsFeedbackDividing

BuddingYeastContactModel

Description: Budding (e.g. budding yeast) cells that - if not dividing - interact with Hertz repulsive contact force and a linearly increasing adhesion force specified with a given rupture force and length. Rupture lenght, rupture force and friction are to be provided as 2x2 matrices, which provide interaction properties as specified by a ‘mask’ array. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

BuddingYeastContactModel (Sphere Sphere)

Budding (e.g. budding yeast) cells that - if not dividing - interact with Hertz repulsive contact force and a linearly increasing adhesion force specified with a given rupture force and length. Rupture lenght, rupture force and friction are to be provided as 2x2 matrices, which provide interaction properties as specified by a ‘mask’ array.

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.
    • F_detach — Symmetric Matrix (NxN) with pull-off force for each interaction type
    • d_detach — Symmetric Matrix (NxN) with rupture lengths for each interaction type
    • division_force — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time — time it takes for the cytokinesis to complete
    • divstiffatt — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • gamma_normal (kg . s^-1) — Symmetric Matrix (NxN) with normal damping for each interaction type (N*s/m)
    • gamma_tangential (kg . s^-1) — Symmetric Matrix (NxN) with tangential damping for each interaction type (N*s/m)
    • mask1 — Array with ‘mask’ indices for pc1
    • mask2 — Array with ‘mask’ indices for pc1
    • 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.
    • state_bud — State value of the bud.
    • state_mother — State value of the mother cell.
  • 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!
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
  • Read only properties:
    • Ehat — Combined Young’s modulus (read-only)

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

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepMaskArrayDataSphere0_2_DataSphere0_1_DataSphere_SphereN_BuddingN_HertzN_MaskedLinearAdhesionForce  <2 >
  ↓
N_T_MaskedConstantResistance  <2 >
  ↓
N_T_ConstantStiffnessN_DividingResistanceAssembleForcesComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContactsFeedbackDividing

ContractileRepulsiveHertzDividingMatrix

Description: Linear contractility up to a user-specified overlap, after which repulsion follows a power-law slope added with an even increased repulsion (Hertz-like) at the point of zero contractility. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

ContractileRepulsiveHertzDividingMatrix (Sphere Sphere)

Linear contractility up to a user-specified overlap, after which repulsion follows a power-law slope added with an even increased repulsion (Hertz-like) at the point of zero contractility.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E1 — Youngs modulus for hard-core repulsion material 1.
    • E2 — Youngs modulus for hard-core repulsion material 2.
    • Wa — Cell-matrix adhesion energy
    • Wc — Contractile energy
    • division_force (kg . m . s^-2) — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time (s) — time it takes for the cytokinesis to complete
    • divstiffatt (kg . s^-2) — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep (kg . s^-2) — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • gamma_normal (kg . s^-1) — Normal friction coefficient (kg/s)
    • gamma_tangential (kg . s^-1) — Tangential friction coefficient (kg/s)
    • nu1 — Poisson ratio for hard-core repulsion material 1.
    • nu2 — Poisson ratio for hard-core repulsion 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.
    • state_dividing — State value of cell which indicates that the cell is currently dividing.
  • 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!
    • 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_SphereN_DividingN_Contractile_HertzN_T_ConstantResistanceN_DividingResistanceAssembleForcesAssemble_ContactArea_2Assemble_ContactArea_1Assemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackFeedbackDividing

DivideAndDieJKRMatrix

Description: Contact model for symmetrically dividing cells, with JKR interactions. Contact forces and friction elements are reduced for dying cells (‘alive_fraction’< 1). We assemble virial stress to the ‘stress’ array and the ‘lost’ volume due to sphere overlap into the ‘volume_loss’ array. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

DivideAndDieJKRMatrix (Sphere Sphere)

Contact model for symmetrically dividing cells, with JKR interactions. Contact forces and friction elements are reduced for dying cells (‘alive_fraction’< 1). We assemble virial stress to the ‘stress’ array and the ‘lost’ volume due to sphere overlap into the ‘volume_loss’ array.

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.
    • division_force (kg . m . s^-2) — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time (s) — time it takes for the cytokinesis to complete
    • divstiffatt (kg . s^-2) — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep (kg . s^-2) — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • 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.
    • state_dividing — State value of cell which indicates that the cell is currently dividing.
  • 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_SphereN_DividingSingleValue_Property  <double >
  ↓
N_JKRN_T_AreaWeightedResistanceN_DividingResistanceModifyForceAndFriction_AliveFractionAssembleForcesAssemble_VirialStressAssemble_VolumeLoss_1Assemble_VolumeLoss_2ComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContactsFeedbackDividing

DivideAndDieLinearAdhesionMatrix

Description: Contact model for symmetrically dividing cells (Experimental). Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

DivideAndDieLinearAdhesionMatrix (Sphere Sphere)

Contact model for symmetrically dividing cells (Experimental).

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.
    • division_force (kg . m . s^-2) — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time (s) — time it takes for the cytokinesis to complete
    • divstiffatt (kg . s^-2) — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep (kg . s^-2) — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • gamma_normal (kg . s^-1) — Normal friction coefficient (kg/s)
    • gamma_tangential (kg . s^-1) — Tangential friction coefficient (kg/s)
    • 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.
    • state_dividing — State value of cell which indicates that the cell is currently dividing.
  • Optional keywords:
    • F_detach1 (kg . m . s^-2) (default value = 0) — Detachment force for pc1
    • F_detach2 (kg . m . s^-2) (default value = 0) — Detachment force for pc2
    • _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!
    • d_detach1 (m) (default value = 0) — Rupture length for pc1
    • d_detach2 (m) (default value = 0) — Rupture length for pc2
    • d_detach (m) (default value = -1) — Rupture length (If not given, we will try to use the values d_detach1 and d_detach2 which are given either as single properties or can be Scalar arrays for pc1 and pc2).
    • f_detach (kg . m . s^-2) (default value = -1) — Detachment force (If not given, we will try to use the values F_detach1 and F_detach2 which are given either as single properties or can be Scalar arrays for pc1 and pc2).
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
  • Read only properties:
    • Ehat — Combined Young’s modulus (read-only)

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

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereN_DividingN_HertzSingleValue_Property  <double >
  ↓
N_LinearAdhesionForceN_T_ConstantResistanceN_DividingResistanceModifyForceAndFriction_AliveFractionAssembleForcesAssemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContactsFeedbackDividing

DividingHaptotaxisJKRMatrix

Description: Symmetrically dividing cells with haptotaxic long range interaction and JKR contact interaction Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

DividingHaptotaxisJKRMatrix (Sphere Sphere)

Symmetrically dividing cells with haptotaxic long range interaction and JKR contact interaction

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.
    • division_force (kg . m . s^-2) — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time (s) — time it takes for the cytokinesis to complete
    • divstiffatt (kg . s^-2) — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep (kg . s^-2) — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • force — Haptotaxic force. Positive force is attractive interaction!
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • 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
    • state_dividing — State value of cell which indicates that the cell is currently dividing.
  • 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_SphereN_DividingSingleValue_Property  <double >
  ↓
N_JKRHaptotaxisForceN_T_AreaWeightedResistanceN_DividingResistanceAssembleForcesAssemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContactsFeedbackDividing

DividingHaptotaxisVariableJKRMatrix

Description: Symmetrically dividing cells with adhesion strength increasing over time. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

DividingHaptotaxisVariableJKRMatrix (Sphere Sphere)

Symmetrically dividing cells with adhesion strength increasing over time.

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.
    • division_force (kg . m . s^-2) — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time (s) — time it takes for the cytokinesis to complete
    • divstiffatt (kg . s^-2) — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep (kg . s^-2) — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • force — Haptotaxic force. Positive force is attractive interaction!
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • 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
    • state_dividing — State value of cell which indicates that the cell is currently dividing.
  • 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!
    • attrFactorMax (default value = 1) — maximum factor for contact state adhesion modifier
    • attrFactorMin (default value = 1) — minimum factor for contact state adhesion modifier
    • attrFactorTime (default value = 0) — time it takes to linearly increase from attrFactorMin to attrFactorMax
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • init_adhesion_modifier (default value = 0) — If ‘True’, will re-init the adhesion modfier of all current contacts the next execution of this contact model. After that, this property will be automatically re-set to ‘false’ for subsequent iterations.

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

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereN_DividingSingleValue_Property  <double >
  ↓
N_JKRContactAdhesionModifierHaptotaxisForceN_T_AreaWeightedResistanceN_DividingResistanceAssembleForcesAssemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContactsFeedbackDividing

DividingJKRAreaMatrix

Description: Symmetrically dividing cells that - if not dividing - interact with a JKR adhesive/repulsive contact force Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

DividingJKRAreaMatrix (Sphere Sphere)

Symmetrically dividing cells that - if not dividing - interact with a JKR adhesive/repulsive contact force

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.
    • division_force (kg . m . s^-2) — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time (s) — time it takes for the cytokinesis to complete
    • divstiffatt (kg . s^-2) — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep (kg . s^-2) — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • 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.
    • state_dividing — State value of cell which indicates that the cell is currently dividing.
  • 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_SphereN_DividingSingleValue_Property  <double >
  ↓
N_JKRN_T_AreaWeightedResistanceN_DividingResistanceAssembleForcesAssemble_ContactArea_2Assemble_ContactArea_1Assemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContactsFeedbackDividing

DividingJKRArrayPropsMatrix

Description: Symmetrically dividing cells that - if not dividing - interact with a JKR adhesive/repulsive contact force Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

DividingJKRArrayPropsMatrix (Sphere Sphere)

Symmetrically dividing cells that - if not dividing - interact with a JKR adhesive/repulsive contact force

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • E1 — Young modulus material 1.
    • E2 — Young modulus material 2.
    • division_force (kg . m . s^-2) — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time (s) — time it takes for the cytokinesis to complete
    • divstiffatt (kg . s^-2) — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep (kg . s^-2) — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • 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.
    • state_dividing — State value of cell which indicates that the cell is currently dividing.
  • 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 (default value = None) — Adhesion energy of material 1
    • attrConst2 (default value = None) — 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_SphereN_DividingArrayValue_Property  <double >
  ↓
N_JKRN_T_AreaWeightedResistanceN_DividingResistanceAssembleForcesAssemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContactsFeedbackDividing

DividingJKRFreedirMatrix

Description: Symmetrically dividing cells that - if not dividing - interact with a JKR adhesive/repulsive contact force. Assembles a free direction too in a ‘free_dir’ array. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

DividingJKRFreedirMatrix (Sphere Sphere)

Symmetrically dividing cells that - if not dividing - interact with a JKR adhesive/repulsive contact force. Assembles a free direction too in a ‘free_dir’ array.

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.
    • division_force (kg . m . s^-2) — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time (s) — time it takes for the cytokinesis to complete
    • divstiffatt (kg . s^-2) — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep (kg . s^-2) — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • 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.
    • state_dividing — State value of cell which indicates that the cell is currently dividing.
  • 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_SphereN_DividingSingleValue_Property  <double >
  ↓
N_JKRN_T_AreaWeightedResistanceN_DividingResistanceAssembleForcesAssemble_FreeDirectionAssemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContactsFeedbackDividing

DividingJKRMatrix

Description: Symmetrically dividing cells that - if not dividing - interact with a JKR adhesive/repulsive contact force Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

DividingJKRMatrix (Sphere Sphere)

Symmetrically dividing cells that - if not dividing - interact with a JKR adhesive/repulsive contact force

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.
    • division_force (kg . m . s^-2) — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time (s) — time it takes for the cytokinesis to complete
    • divstiffatt (kg . s^-2) — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep (kg . s^-2) — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • 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.
    • state_dividing — State value of cell which indicates that the cell is currently dividing.
  • 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_SphereN_DividingSingleValue_Property  <double >
  ↓
N_JKRN_T_AreaWeightedResistanceN_DividingResistanceAssembleForcesAssemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContactsFeedbackDividing

DividingVariableJKRMatrix

Description: Symmetrically dividing cells with adhesion strength increasing over time. Geometry combinations available:

PC2 | PC1 - Sphere
Sphere YES

DividingVariableJKRMatrix (Sphere Sphere)

Symmetrically dividing cells with adhesion strength increasing over time.

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.
    • division_force (kg . m . s^-2) — Maximum force applied between two dividing cells in order to keep the desired division trajectory
    • division_time (s) — time it takes for the cytokinesis to complete
    • divstiffatt (kg . s^-2) — attractive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • divstiffrep (kg . s^-2) — repulsive stiffness of the cell division controller. If chosen high, the cytokinesis will follow the prescribed trajectory more closely. If chosen too high, might become unstable.
    • gamma_dividing — Normal friction coefficient for dividing cells (kg/s).
    • 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.
    • state_dividing — State value of cell which indicates that the cell is currently dividing.
  • 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!
    • attrFactorMax (default value = 1) — maximum factor for contact state adhesion modifier
    • attrFactorMin (default value = 1) — minimum factor for contact state adhesion modifier
    • attrFactorTime (default value = 0) — time it takes to linearly increase from attrFactorMin to attrFactorMax
    • implicitness (default value = 0) — Choose the semi-implicit integration method. (0 for explicit Euler, 1 for implicit Euler, 0.5 for Cranck-Nicholson).
    • init_adhesion_modifier (default value = 0) — If ‘True’, will re-init the adhesion modfier of all current contacts the next execution of this contact model. After that, this property will be automatically re-set to ‘false’ for subsequent iterations.

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

DefaultBoilerPlateContactMatrixDataBoilerPlateContactMatrixContactStateKeepTimeStepSphere0_2_DataSphere0_1_DataSphere_SphereN_DividingSingleValue_Property  <double >
  ↓
N_JKRContactAdhesionModifierN_T_AreaWeightedResistanceN_DividingResistanceAssembleForcesAssemble_VirialStressComputeContactMatrixElementOverdampedAssembleContactMatrixFeedbackKeepContactsFeedbackDividing