def calcForce(positions, numberOfCells, numberOfdead, Origin, oriConc,
cellConc, Diff, t, kd, highBC, DisplacementScaleByConc,
searchingRange, marker, auto_factor, state, ConcByCell, odes,
step_size, shape_factor):
'''
[Parameter Description]
positions: position of cells from pdb file
numberOfCells: total number of cells (num of cells in 1st half + num of cells in 2nd half)
Origin: the origin of chemoattractant source
oriConc: the max concentration released from the source of chemoattractant
cellConc: the max concentration released by cells (determining the degree of intercellular communication)
Diff: the diffusion rate of chemoattractant
t: time
kd: constant associated with Hills coefficient for autocrinic release
highBC: [max X, max Y, max Z]
DisplacementScaleByConc: Displacement Scale
searchingRange: searching range around the cell
marker: a list of marker for resting and activated cells
auto_factor: a list of autocrinic factors based on the state of cells
state: the characteristics of diffusion of chemoattractant: steady, error, or linear
ConcByCell: the concentration accumulated by the attractant released from each individual cell
shape_factor: = 1 for square > 1 for slab
'''
# Do some magic here that will return substrate field-related force acting on each particle
n = 0
m = 0
dummy_coord = np.zeros([numberOfCells, 2]) # since it's 2D
for i in enumerate(positions):
if n > numberOfdead:
dummy_coord[m][0] = i[1][0].value_in_unit(nanometers)
dummy_coord[m][1] = i[1][1].value_in_unit(nanometers)
#dummy_coord[m][2] = i[1][2].value_in_unit(nanometers)*0
m += 1
n += 1
recordedPositions = dummy_coord
# Done
DistCelltoOrigin = conc.DistCelltoOrigin(recordedPositions, Origin,
shape_factor, state)
# Done
DistCelltoCell = conc.DistCelltoCell(recordedPositions)
# Done
ConcByOrigin = conc.ConcByOrigin(DistCelltoOrigin, t, Diff, oriConc, state,
Origin)
# Done
ConcbyCell, HC = conc.ConcByCell(ConcByOrigin, ConcByCell, DistCelltoCell,
t, Diff, kd, auto_factor, cellConc)
fvX, fvY, fvZ, odesnew = conc.forceGen(ConcbyCell, Origin, shape_factor,
recordedPositions, t, Diff, HC,
searchingRange, highBC,
DisplacementScaleByConc, cellConc,
oriConc, state, odes, step_size)
return fvX, fvY, fvZ, ConcbyCell, odesnew
def calcForce(positions, numberOfCells, Origin, SourceOfOrigin, oriConc,
cellConc, Diff, t, kd, highBC, DisplacementScaleByConc,
searchingRange, marker, auto_factor, state, ConcByCell):
'''
[Parameter Description]
positions: position of cells from pdb file
numberOfCells: total number of cells (num of cells in 1st half + num of cells in 2nd half)
Origin: the origin of chemoattractant source
SourceOfOrigin: None = One end of simulation box in x axis, Center = the center of simulation box
oriConc: the max concentration released from the source of chemoattractant
cellConc: the max concentration released by cells (determining the degree of intercellular communication)
Diff: the diffusion rate of chemoattractant
t: time
kd: constant associated with Hills coefficient for autocrinic release
highBC: [max X, max Y, max Z]
DisplacementScaleByConc: Displacement Scale
searchingRange: searching range around the cell
marker: a list of marker for resting and activated cells
auto_factor: a list of autocrinic factors based on the state of cells
state: the characteristics of diffusion of chemoattractant: steady, error, or linear
ConcByCell: the concentration accumulated by the attractant released from each individual cell
'''
# Do some magic here that will return substrate field-related force acting on each particle
n = 0
dummy_coord = np.zeros([3, numberOfCells])
#ConcByCell = np.zeros(numberOfCells) + 1e-14
for i in enumerate(positions):
dummy_coord[0][n] = i[1][0].value_in_unit(nanometers)
dummy_coord[1][n] = i[1][1].value_in_unit(nanometers)
dummy_coord[2][n] = i[1][2].value_in_unit(nanometers) * 0
n += 1
recordedPositions = dummy_coord
DistCelltoOrigin = conc.DistCelltoOrigin(recordedPositions, Origin,
SourceOfOrigin, state)
DistCelltoCell = conc.DistCelltoCell(recordedPositions)
ConcByOrigin = conc.ConcByOrigin(DistCelltoOrigin, t, Diff, oriConc, state,
Origin)
ConcbyCell, HC = conc.ConcByCell(ConcByOrigin, ConcByCell, DistCelltoCell,
t, Diff, kd, auto_factor, cellConc)
fvX, fvY, fvZ = conc.forceGen(ConcbyCell, Origin, SourceOfOrigin,
recordedPositions, t, Diff, HC,
searchingRange, highBC,
DisplacementScaleByConc, cellConc, oriConc,
state)
return fvX, fvY, fvZ, ConcbyCell