tyssue.dynamics package#
Submodules#
tyssue.dynamics.apoptosis_model module#
Specific functions for apoptosis vertex model
- class tyssue.dynamics.apoptosis_model.ApicoBasalTension[source]#
Bases:
AbstractEffector
Effector for the apical-basal tension.
The energy is proportional to the heigth of the cell
- dimensions = array(1.) * fJ/um**2#
- element = 'vert'#
- label = 'Apical-basal tension'#
- magnitude = 'radial_tension'#
- specs = {'vert': {'height': 1.0, 'is_active': 1, 'radial_tension': 0.0}}#
tyssue.dynamics.base_gradients module#
tyssue.dynamics.bulk_gradients module#
Base gradients for bulk geometry
- tyssue.dynamics.bulk_gradients.lumen_volume_grad(eptm)[source]#
Calculates the gradient for the volume enclosed by the epithelium.
For a monolayer, it will by default compute the volume enclosed by the basal side (edges whose ‘segment’ column is “basal”). If the polarity is reversed and the apical side faces the lumen, this can be changed by setting eptm.settings[“lumen_side”] to ‘apical’
tyssue.dynamics.bulk_model module#
Dynamical models for monlayer and bulk epithelium.
tyssue.dynamics.effectors module#
Generic forces and energies
- class tyssue.dynamics.effectors.AbstractEffector[source]#
Bases:
object
The effector class is used by model factories to construct a model.
- dimensions = None#
- element = None#
- label = 'Abstract effector'#
- magnitude = None#
- spatial_ref = (None, None)#
- specs = {'cell': {}, 'edge': {}, 'face': {}, 'vert': {}}#
- temporal_ref = (None, None)#
- class tyssue.dynamics.effectors.BarrierElasticity[source]#
Bases:
AbstractEffector
Barrier use to maintain the tissue integrity.
- dimensions = array(1.) * fJ/um**2#
- element = 'vert'#
- label = 'Barrier elasticity'#
- magnitude = 'barrier_elasticity'#
- specs = {'vert': {'barrier_elasticity': 1.0, 'delta_rho': 0.0, 'is_active': 1}}#
- class tyssue.dynamics.effectors.BorderElasticity[source]#
Bases:
AbstractEffector
- dimensions = array(1.) * fJ/um**2#
- element = 'edge'#
- label = 'Border edges elasticity'#
- magnitude = 'border_elasticity'#
- spatial_ref = ('prefered_length', UnitLength('micrometer', 0.001 * mm, 'um'))#
- specs = {'edge': {'border_elasticity': 1.0, 'is_active': 1, 'is_border': 1.0, 'length': 1.0, 'prefered_length': 1.0}}#
- class tyssue.dynamics.effectors.CellAreaElasticity[source]#
Bases:
AbstractEffector
- dimensions = array(1.) * fJ/um**4#
- element = 'cell'#
- label = 'Area elasticity'#
- magnitude = 'area_elasticity'#
- spatial_ref = ('prefered_area', array(1.) * um**2)#
- specs = {'cell': {'area': 1.0, 'area_elasticity': 1.0, 'is_alive': 1, 'prefered_area': 1.0}}#
- class tyssue.dynamics.effectors.CellVolumeElasticity[source]#
Bases:
AbstractEffector
- dimensions = array(1.) * fJ/um**6#
- element = 'cell'#
- label = 'Volume elasticity'#
- magnitude = 'vol_elasticity'#
- spatial_ref = ('prefered_vol', array(1.) * um**3)#
- specs = {'cell': {'is_alive': 1, 'prefered_vol': 1.0, 'vol': 1.0, 'vol_elasticity': 1.0}}#
- class tyssue.dynamics.effectors.FaceAreaElasticity[source]#
Bases:
AbstractEffector
- dimensionless = False#
- dimensions = array(1.) * fJ/um**4#
- element = 'face'#
- label = 'Area elasticity'#
- magnitude = 'area_elasticity'#
- spatial_ref = ('prefered_area', array(1.) * um**2)#
- specs = {'edge': {'sub_area': 0.16666666666666666}, 'face': {'area': 1.0, 'area_elasticity': 1.0, 'is_alive': 1, 'prefered_area': 1.0}}#
- class tyssue.dynamics.effectors.FaceContractility[source]#
Bases:
AbstractEffector
- dimensions = array(1.) * fJ/um**2#
- element = 'face'#
- label = 'Contractility'#
- magnitude = 'contractility'#
- spatial_ref = ('mean_perimeter', UnitLength('micrometer', 0.001 * mm, 'um'))#
- specs = {'face': {'contractility': 1.0, 'is_alive': 1, 'perimeter': 1.0}}#
- class tyssue.dynamics.effectors.FaceVolumeElasticity[source]#
Bases:
AbstractEffector
- dimensions = array(1.) * fJ/um**6#
- element = 'face'#
- label = 'Volume elasticity'#
- magnitude = 'vol_elasticity'#
- spatial_ref = ('prefered_vol', array(1.) * um**3)#
- specs = {'edge': {'sub_area': 0.16666666666666666}, 'face': {'is_alive': 1, 'prefered_vol': 1.0, 'vol': 1.0, 'vol_elasticity': 1.0}, 'vert': {'height': 1.0}}#
- class tyssue.dynamics.effectors.LengthElasticity[source]#
Bases:
AbstractEffector
Elastic half edge
- dimensions = array(1.) * fJ/um**2#
- element = 'edge'#
- label = 'Length elasticity'#
- magnitude = 'length_elasticity'#
- spatial_ref = ('prefered_length', UnitLength('micrometer', 0.001 * mm, 'um'))#
- specs = {'edge': {'is_active': 1, 'length': 1.0, 'length_elasticity': 1.0, 'prefered_length': 1.0, 'ux': 0.5773502691896257, 'uy': 0.5773502691896257, 'uz': 0.5773502691896257}}#
- class tyssue.dynamics.effectors.LineTension[source]#
Bases:
AbstractEffector
- dimensions = array(1.) * fJ/um#
- element = 'edge'#
- label = 'Line tension'#
- magnitude = 'line_tension'#
- spatial_ref = ('mean_length', UnitLength('micrometer', 0.001 * mm, 'um'))#
- specs = {'edge': {'is_active': 1, 'line_tension': 1.0}}#
- class tyssue.dynamics.effectors.LineViscosity[source]#
Bases:
AbstractEffector
- dimensions = array(1.) * s*nN/um#
- element = 'edge'#
- label = 'Linear viscosity'#
- magnitude = 'edge_viscosity'#
- spatial_ref = ('mean_length', UnitLength('micrometer', 0.001 * mm, 'um'))#
- specs = {'edge': {'edge_viscosity': 1.0, 'is_active': 1}}#
- temporal_ref = ('dt', UnitTime('second', 's'))#
- class tyssue.dynamics.effectors.LumenAreaElasticity[source]#
Bases:
AbstractEffector
..math:
rac{K_Y}{2}(A_{mathrm{lumen}} - A_{0,mathrm{lumen}})^2
- dimensions = array(1.) * fJ/um**4#
- element = 'settings'#
- label = 'Lumen volume constraint'#
- magnitude = 'lumen_elasticity'#
- spatial_ref = ('lumen_prefered_vol', array(1.) * um**2)#
- specs = {'settings': {'lumen_elasticity': 1.0, 'lumen_prefered_vol': 1.0, 'lumen_vol': 1.0}}#
- class tyssue.dynamics.effectors.LumenVolumeElasticity[source]#
Bases:
AbstractEffector
Global volume elasticity of the object. For example the volume of the yolk in the Drosophila embryo
- dimensions = array(1.) * fJ/um**6#
- element = 'settings'#
- label = 'Lumen volume elasticity'#
- magnitude = 'lumen_vol_elasticity'#
- spatial_ref = ('lumen_prefered_vol', array(1.) * um**3)#
- specs = {'settings': {'lumen_prefered_vol': 1.0, 'lumen_vol': 1.0, 'lumen_vol_elasticity': 1.0}}#
- class tyssue.dynamics.effectors.MidlineBoundary[source]#
Bases:
AbstractEffector
Elastic boundary at the x-axis, to be used with MidlineBoundaryGeometry. Intended to use with a high midline_boundary_stiffness to prevent vertices from crossing the midline.
- dimensions = array(1.) * fJ/um**2#
- element = 'vert'#
- label = 'Midline boundary'#
- magnitude = 'midline_boundary'#
- specs = {'vert': {'boundary_K': 280, 'delta_boundary': 0, 'is_active': 1}}#
- class tyssue.dynamics.effectors.PerimeterElasticity[source]#
Bases:
AbstractEffector
From Mapeng Bi et al. https://doi.org/10.1038/nphys3471
- dimensions = array(1.) * fJ/um**2#
- element = 'face'#
- label = 'Perimeter Elasticity'#
- magnitude = 'perimeter_elasticity'#
- spatial_ref = ('prefered_perimeter', UnitLength('micrometer', 0.001 * mm, 'um'))#
- specs = {'face': {'is_alive': 1, 'perimeter': 1.0, 'perimeter_elasticity': 0.1, 'prefered_perimeter': 3.81}}#
- class tyssue.dynamics.effectors.RadialTension[source]#
Bases:
AbstractEffector
Apply a tension perpendicular to a face.
- dimensions = array(1.) * fJ/um#
- element = 'face'#
- label = 'Apical basal tension'#
- magnitude = 'radial_tension'#
- specs = {'face': {'height': 1.0, 'radial_tension': 1.0}}#
- class tyssue.dynamics.effectors.SurfaceTension[source]#
Bases:
AbstractEffector
- dimensions = array(1.) * fJ/um**2#
- element = 'face'#
- label = 'Surface tension'#
- magnitude = 'surface_tension'#
- spatial_ref = ('prefered_area', array(1.) * um**2)#
- specs = {'face': {'area': 1.0, 'is_active': 1, 'surface_tension': 1.0}}#
tyssue.dynamics.factory module#
- tyssue.dynamics.factory.model_factory(effectors, ref_effector=None)[source]#
Produces a Model class with the provided effectors.
- Parameters
effectors (list of
effectors.AbstractEffectors
classes.) –ref_effector (optional, default None) – if passed, will be used for normalization, by default, the last effector in the list is used
- Returns
NewModel – methods
- Return type
a Model derived class with compute_enregy and compute_gradient
tyssue.dynamics.planar_gradients module#
tyssue.dynamics.planar_vertex_model module#
tyssue.dynamics.sheet_gradients module#
Base gradients for sheet like geometries
tyssue.dynamics.sheet_vertex_model module#
Vertex model for an Epithelial sheet (see definitions).
Depends on the sheet vertex geometry functions.
tyssue.dynamics.units module#
Small module to manage units and dimension analysis
Module contents#
dynamics