mpacts.contact.models.misc. focaladhesions

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

import mpacts.contact.models.misc.focaladhesions
#or assign it to a shorter name
import mpacts.contact.models.misc.focaladhesions as foc

FocalAdhBellImbRefractory

Description: A model that creates focal adhesions between nodes on a cell and a point determined by projecting the node on the triangles constituting a substrate plane. Focal adhesion consists of two Hookean springs in series, one representing the adhesion complex itself and the other the extracellular matrix (ECM). Thus displacement of the cellular node bound to the substrate is dependent on ECM spring stiffness. Model also updates adhesion, going through existing adhesions and checks if they remain bound or break loose based on a probability. This probability depends on the force carried by the adhesion (Bell model), thus the model stores the force in the contact state. Cell node array end Cell determines different probability of FA disassembly (multiplying factor). After an adhesion breaks, the node cannot form a new adhesion for a refractory period. Geometry combinations available:

PC2 | PC1 - Rigid_Triangle
Sphere YES

FocalAdhBellImbRefractory (Rigid_Triangle Sphere)

A model that creates focal adhesions between nodes on a cell and a point determined by projecting the node on the triangles constituting a substrate plane. Focal adhesion consists of two Hookean springs in series, one representing the adhesion complex itself and the other the extracellular matrix (ECM). Thus displacement of the cellular node bound to the substrate is dependent on ECM spring stiffness. Model also updates adhesion, going through existing adhesions and checks if they remain bound or break loose based on a probability. This probability depends on the force carried by the adhesion (Bell model), thus the model stores the force in the contact state. Cell node array end Cell determines different probability of FA disassembly (multiplying factor). After an adhesion breaks, the node cannot form a new adhesion for a refractory period.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • Fr — rupture force
    • Fzeta — parameter by which F is divided to determine probability of detachment
    • Lmthr — value of LmID above which node is in lamellum (0-1)
    • Lo_max — maximum extension of system allowed at formation
    • Lsys — resting length two spring system
    • keq — equivalent stiffness of two springs
    • 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.
    • pf_FA — factor describing probability of formation of a FA
    • pr_FA — factor describing probability of disassembly of a FA
    • t_mat — time period after which a FA is considered mature and when rupturing cortex must undergo rebuilding (t_ref)
    • t_ref — time period after an adhesion is broken or disassembled in which no other can be formed at a node
    • zeta — factor determining drop of probability with increasing adhesion force
  • Optional keywords:
    • Fprim1 (default value = None) — Array with vectors which stores the contact force per primitive for pc1. If not given, the array pc1[‘Fprim’] is searched first, and if not found, nothing will be done
    • flip_normals (default value = 0) — If ‘True’, the normals of the N-Gon will be flipped.In most cases, we recommend that you leave this option to its default ‘false’. Contrary to the option ‘flip_normals’ in e.g. Ngon-Sphere contact, this option will always flip the normals, if enables, since points do not have any radius.

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

RoundedTriangleBoilerPlateRigid_NGon_1_Data  <3 >
  ↓
Point_2_DataNGon_PointFocalAdhBellImbRefractoryAssembleForces_1AssembleForces_2AssembleForces_Primitives_1FeedbackKeepContacts

FocalAdhImbRefractory

Description: A model that creates focal adhesions between nodes on a cell and a point determined by projecting the node on the triangles constituting a substrate plane. Focal adhesion consists of two Hookean springs in series, one representing the adhesion complex itself and the other the extracellular matrix (ECM). Thus displacement of the cellular node bound to the substrate is dependent on ECM spring stiffness. Model also updates adhesion, going through existing adhesions and checks if they remain bound or break loose based on a probability. The probability of disassembly is independent of force and passed as a parameter. The model stores the force in the contact state. Cell node array end Cell determines different probability of FA disassembly (multiplying factor). Geometry combinations available:

PC2 | PC1 - Rigid_Triangle
Sphere YES

FocalAdhImbRefractory (Rigid_Triangle Sphere)

A model that creates focal adhesions between nodes on a cell and a point determined by projecting the node on the triangles constituting a substrate plane. Focal adhesion consists of two Hookean springs in series, one representing the adhesion complex itself and the other the extracellular matrix (ECM). Thus displacement of the cellular node bound to the substrate is dependent on ECM spring stiffness. Model also updates adhesion, going through existing adhesions and checks if they remain bound or break loose based on a probability. The probability of disassembly is independent of force and passed as a parameter. The model stores the force in the contact state. Cell node array end Cell determines different probability of FA disassembly (multiplying factor).

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • Fr — rupture force
    • Lmthr — value of LmID above which node is in lamellum (0-1)
    • Lo_max — maximum extension of system allowed at formation
    • Lsys — resting length two spring system
    • keq — equivalent stiffness of two springs
    • 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.
    • pf_FA — factor describing probability of formation of a FA
    • pr_FA — factor describing probability of disassembly of a FA
    • t_mat — time period after which a FA is considered mature and when rupturing cortex must undergo rebuilding (t_ref)
    • t_ref — time period after an adhesion is broken or disassembled in which no other can be formed at a node
  • Optional keywords:
    • Fprim1 (default value = None) — Array with vectors which stores the contact force per primitive for pc1. If not given, the array pc1[‘Fprim’] is searched first, and if not found, nothing will be done
    • flip_normals (default value = 0) — If ‘True’, the normals of the N-Gon will be flipped.In most cases, we recommend that you leave this option to its default ‘false’. Contrary to the option ‘flip_normals’ in e.g. Ngon-Sphere contact, this option will always flip the normals, if enables, since points do not have any radius.

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

RoundedTriangleBoilerPlateRigid_NGon_1_Data  <3 >
  ↓
Point_2_DataNGon_PointFocalAdhImbRefractoryAssembleForces_1AssembleForces_2AssembleForces_Primitives_1FeedbackKeepContacts

FocalAdhesion

Description: A model that creates focal adhesions between nodes on a cell and a point determined by projecting the node on the triangles constituting a substrate plane. Focal adhesion in the form of a Hookean spring. Model also updates adhesion, going through existing adhesions and checks if they remain bound or break loose based on a probability. The model stores the force in the contact state. Geometry combinations available:

PC2 | PC1 - Rigid_Triangle
Sphere YES

FocalAdhesion (Rigid_Triangle Sphere)

A model that creates focal adhesions between nodes on a cell and a point determined by projecting the node on the triangles constituting a substrate plane. Focal adhesion in the form of a Hookean spring. Model also updates adhesion, going through existing adhesions and checks if they remain bound or break loose based on a probability. The model stores the force in the contact state.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • Lc — resting length
    • Lr — rupture length
    • c — spring constant
    • 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.
    • pf_FA — factor describing probability of formation of a FA
    • pr_FA — factor describing probability of disassembly of a FA
  • Optional keywords:
    • Fprim1 (default value = None) — Array with vectors which stores the contact force per primitive for pc1. If not given, the array pc1[‘Fprim’] is searched first, and if not found, nothing will be done
    • flip_normals (default value = 0) — If ‘True’, the normals of the N-Gon will be flipped.In most cases, we recommend that you leave this option to its default ‘false’. Contrary to the option ‘flip_normals’ in e.g. Ngon-Sphere contact, this option will always flip the normals, if enables, since points do not have any radius.

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

RoundedTriangleBoilerPlateRigid_NGon_1_Data  <3 >
  ↓
Point_2_DataNGon_PointFocalAdhesionAssembleForces_1AssembleForces_2AssembleForces_Primitives_1FeedbackKeepContacts

FocalAdhesionBell

Description: A model that creates focal adhesions between nodes on a cell and a point determined by projecting the node on the triangles constituting a substrate plane. Focal adhesion consists of two Hookean springs in series, one representing the adhesion complex itself and the other the extracellular matrix (ECM). Thus displacement of the cellular node bound to the substrate is dependent on ECM spring stiffness. Model also updates adhesion, going through existing adhesions and checks if they remain bound or break loose based on a probability. This probability depends on the force carried by the adhesion (Bell model), thus the model stores the force in the contact state. Geometry combinations available:

PC2 | PC1 - Rigid_Triangle
Sphere YES

FocalAdhesionBell (Rigid_Triangle Sphere)

A model that creates focal adhesions between nodes on a cell and a point determined by projecting the node on the triangles constituting a substrate plane. Focal adhesion consists of two Hookean springs in series, one representing the adhesion complex itself and the other the extracellular matrix (ECM). Thus displacement of the cellular node bound to the substrate is dependent on ECM spring stiffness. Model also updates adhesion, going through existing adhesions and checks if they remain bound or break loose based on a probability. This probability depends on the force carried by the adhesion (Bell model), thus the model stores the force in the contact state.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • Fr — rupture force
    • Fzeta — parameter by which F is divided to determine probability of detachment
    • Lmthr — value of LmID above which node is in lamellum (0-1)
    • Lo_max — maximum extension of system allowed at formation
    • Lsys — resting length two spring system
    • keq — equivalent stiffness of two springs
    • 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.
    • pf_FA — factor describing probability of formation of a FA
    • pr_FA — factor describing probability of disassembly of a FA
    • zeta — factor determining drop of probability with increasing adhesion force
  • Optional keywords:
    • Fprim1 (default value = None) — Array with vectors which stores the contact force per primitive for pc1. If not given, the array pc1[‘Fprim’] is searched first, and if not found, nothing will be done
    • flip_normals (default value = 0) — If ‘True’, the normals of the N-Gon will be flipped.In most cases, we recommend that you leave this option to its default ‘false’. Contrary to the option ‘flip_normals’ in e.g. Ngon-Sphere contact, this option will always flip the normals, if enables, since points do not have any radius.

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

RoundedTriangleBoilerPlateRigid_NGon_1_Data  <3 >
  ↓
Point_2_DataNGon_PointFocalAdhesionBellAssembleForces_1AssembleForces_2AssembleForces_Primitives_1FeedbackKeepContacts

FocalAdhesionBellImb

Description: A model that creates focal adhesions between nodes on a cell and a point determined by projecting the node on the triangles constituting a substrate plane. Focal adhesion consists of two Hookean springs in series, one representing the adhesion complex itself and the other the extracellular matrix (ECM). Thus displacement of the cellular node bound to the substrate is dependent on ECM spring stiffness. Model also updates adhesion, going through existing adhesions and checks if they remain bound or break loose based on a probability. This probability depends on the force carried by the adhesion (Bell model), thus the model stores the force in the contact state. Cell node array end Cell determines different probability of FA disassembly (multiplying factor). Geometry combinations available:

PC2 | PC1 - Rigid_Triangle
Sphere YES

FocalAdhesionBellImb (Rigid_Triangle Sphere)

A model that creates focal adhesions between nodes on a cell and a point determined by projecting the node on the triangles constituting a substrate plane. Focal adhesion consists of two Hookean springs in series, one representing the adhesion complex itself and the other the extracellular matrix (ECM). Thus displacement of the cellular node bound to the substrate is dependent on ECM spring stiffness. Model also updates adhesion, going through existing adhesions and checks if they remain bound or break loose based on a probability. This probability depends on the force carried by the adhesion (Bell model), thus the model stores the force in the contact state. Cell node array end Cell determines different probability of FA disassembly (multiplying factor).

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • Fr — rupture force
    • Fzeta — parameter by which F is divided to determine probability of detachment
    • Lmthr — value of LmID above which node is in lamellum (0-1)
    • Lo_max — maximum extension of system allowed at formation
    • Lsys — resting length two spring system
    • keq — equivalent stiffness of two springs
    • 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.
    • pf_FA — factor describing probability of formation of a FA
    • pr_FA — factor describing probability of disassembly of a FA
    • zeta — factor determining drop of probability with increasing adhesion force
  • Optional keywords:
    • Fprim1 (default value = None) — Array with vectors which stores the contact force per primitive for pc1. If not given, the array pc1[‘Fprim’] is searched first, and if not found, nothing will be done
    • flip_normals (default value = 0) — If ‘True’, the normals of the N-Gon will be flipped.In most cases, we recommend that you leave this option to its default ‘false’. Contrary to the option ‘flip_normals’ in e.g. Ngon-Sphere contact, this option will always flip the normals, if enables, since points do not have any radius.

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

RoundedTriangleBoilerPlateRigid_NGon_1_Data  <3 >
  ↓
Point_2_DataNGon_PointFocalAdhesionBellImbAssembleForces_1AssembleForces_2AssembleForces_Primitives_1FeedbackKeepContacts

FocalAdhesionSubs

Description: A model that creates focal adhesions between nodes on a cell and a point determined by projecting the node on the triangles constituting a substrate plane. Focal adhesion consists of two Hookean springs in series, one representing the adhesion complex itself and the other the extracellular matrix (ECM). Thus displacement of the cellular node bound to the substrate is dependent on ECM spring stiffness. Model also updates adhesion, going through existing adhesions and checks if they remain bound or break loose based on a probability. The model stores the force in the contact state. Geometry combinations available:

PC2 | PC1 - Rigid_Triangle
Sphere YES

FocalAdhesionSubs (Rigid_Triangle Sphere)

A model that creates focal adhesions between nodes on a cell and a point determined by projecting the node on the triangles constituting a substrate plane. Focal adhesion consists of two Hookean springs in series, one representing the adhesion complex itself and the other the extracellular matrix (ECM). Thus displacement of the cellular node bound to the substrate is dependent on ECM spring stiffness. Model also updates adhesion, going through existing adhesions and checks if they remain bound or break loose based on a probability. The model stores the force in the contact state.

Parallel Compatible: Yes

Properties:

  • Required keywords:
    • Fr — rupture force
    • Lo_max — maximum extension of system allowed at formation
    • Lsys — resting length two spring system
    • keq — equivalent stiffness two springs
    • 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.
    • pf_FA — factor describing probability of formation of a FA
    • pr_FA — factor describing probability of disassembly of a FA
  • Optional keywords:
    • Fprim1 (default value = None) — Array with vectors which stores the contact force per primitive for pc1. If not given, the array pc1[‘Fprim’] is searched first, and if not found, nothing will be done
    • flip_normals (default value = 0) — If ‘True’, the normals of the N-Gon will be flipped.In most cases, we recommend that you leave this option to its default ‘false’. Contrary to the option ‘flip_normals’ in e.g. Ngon-Sphere contact, this option will always flip the normals, if enables, since points do not have any radius.

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

RoundedTriangleBoilerPlateRigid_NGon_1_Data  <3 >
  ↓
Point_2_DataNGon_PointFocalAdhesionSubsAssembleForces_1AssembleForces_2AssembleForces_Primitives_1FeedbackKeepContacts