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311dea91a9b6
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Merged Roeland's latest changes with my project file changes (16:3f0977faba37).
--
user: Michael Guravage <michael.guravage@cwi.nl>
branch merge
branch 'default'
changed src/Makefile
changed src/TutorialCode/Tutorial0/mymodel.cpp
changed src/TutorialCode/Tutorial0/mymodel.h
changed src/TutorialCode/Tutorial0/mymodel.pro
changed src/TutorialCode/Tutorial1/mymodel.cpp
changed src/TutorialCode/Tutorial1/mymodel.h
changed src/TutorialCode/Tutorial1/mymodel.pro
changed src/TutorialCode/Tutorial2/mymodel.cpp
changed src/TutorialCode/Tutorial2/mymodel.h
changed src/TutorialCode/Tutorial2/mymodel.pro
changed src/TutorialCode/Tutorial3/mymodel.cpp
changed src/TutorialCode/Tutorial3/mymodel.h
changed src/TutorialCode/Tutorial3/mymodel.pro
changed src/TutorialCode/Tutorial4/mymodel.cpp
changed src/TutorialCode/Tutorial4/mymodel.h
changed src/TutorialCode/Tutorial4/mymodel.pro
changed src/TutorialCode/Tutorial5/mymodel.cpp
changed src/TutorialCode/Tutorial5/mymodel.h
changed src/TutorialCode/Tutorial5/mymodel.pro
changed src/VirtualLeaf.pro
changed src/VirtualLeafpar.tmpl
changed src/build_models/Makefile
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/build_models/leafplugin.cpp
changed src/build_models/leafplugin.h
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/meinhardtplugin.h
changed src/build_models/plugin_auxingrowth.pro
changed src/build_models/plugin_leaf.pro
changed src/build_models/plugin_meinhardt.pro
changed src/build_models/plugin_test.pro
changed src/build_models/testplugin.cpp
changed src/build_models/testplugin.h
changed src/build_models/translate_plugin.pl
changed src/cell.cpp
changed src/cellbase.h
changed src/libplugin.pro
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/simplugin.h
removed src/build_models/simplugin.h
--
user: Michael Guravage <michael.guravage@cwi.nl>
branch merge
branch 'default'
changed src/Makefile
changed src/TutorialCode/Tutorial0/mymodel.cpp
changed src/TutorialCode/Tutorial0/mymodel.h
changed src/TutorialCode/Tutorial0/mymodel.pro
changed src/TutorialCode/Tutorial1/mymodel.cpp
changed src/TutorialCode/Tutorial1/mymodel.h
changed src/TutorialCode/Tutorial1/mymodel.pro
changed src/TutorialCode/Tutorial2/mymodel.cpp
changed src/TutorialCode/Tutorial2/mymodel.h
changed src/TutorialCode/Tutorial2/mymodel.pro
changed src/TutorialCode/Tutorial3/mymodel.cpp
changed src/TutorialCode/Tutorial3/mymodel.h
changed src/TutorialCode/Tutorial3/mymodel.pro
changed src/TutorialCode/Tutorial4/mymodel.cpp
changed src/TutorialCode/Tutorial4/mymodel.h
changed src/TutorialCode/Tutorial4/mymodel.pro
changed src/TutorialCode/Tutorial5/mymodel.cpp
changed src/TutorialCode/Tutorial5/mymodel.h
changed src/TutorialCode/Tutorial5/mymodel.pro
changed src/VirtualLeaf.pro
changed src/VirtualLeafpar.tmpl
changed src/build_models/Makefile
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/build_models/leafplugin.cpp
changed src/build_models/leafplugin.h
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/meinhardtplugin.h
changed src/build_models/plugin_auxingrowth.pro
changed src/build_models/plugin_leaf.pro
changed src/build_models/plugin_meinhardt.pro
changed src/build_models/plugin_test.pro
changed src/build_models/testplugin.cpp
changed src/build_models/testplugin.h
changed src/build_models/translate_plugin.pl
changed src/cell.cpp
changed src/cellbase.h
changed src/libplugin.pro
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/simplugin.h
removed src/build_models/simplugin.h
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 | /*
*
* This file is part of the Virtual Leaf.
*
* The Virtual Leaf is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The Virtual Leaf is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with the Virtual Leaf. If not, see <http://www.gnu.org/licenses/>.
*
* Copyright 2010 Roeland Merks.
*
*/
#include <QObject>
#include <QtGui>
#include "simplugin.h"
#include "parameter.h"
#include "wallbase.h"
#include "cellbase.h"
#include "leafplugin.h"
#include "far_mem_5.h"
static const std::string _module_id("$Id$");
bool batch = false;
// To be executed after cell division
void LeafPlugin::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
// PIN1 distributes between parent and daughter according to area
double area = daughter1->Area(), daughter_area = daughter2->Area();
double tot_area = area + daughter_area;
//chem[1]*=(area/tot_area);
//daughter.chem[1]*=(daughter_area/tot_area);
// For lack of detailed data, or a better rule, we assume that cells remain polarized
// after division
// So the PIN1 is redistributed according to the original polarization over the walls
// parent_info contains info about the parent
// redistribute the PIN in the endosome according to area
// "Fudge" rule: if one of the cells is at the boundary, remove all AUX1 in the other cell
if (daughter1->AtBoundaryP() && !daughter2->AtBoundaryP()) {
//daughter2->new_chem[2]=daughter2->chem[2]=0.;
daughter2->SetNewChem(2,0);
daughter2->SetChemical(2,0);
//daughter.new_chem[0]=daughter.chem[0]=0.;
//cerr << "Clearing daughter\n";
//for (list<Wall *>::const_iterator w=daughter.walls.begin();
// w!=daughter.walls.end();
// w++) {
// (*w)->setTransporter(&daughter, 1, 0.);
//}
//new_chem[2]=chem[2]=parent_info->PINendosome;
daughter1->SetNewChem(2,parent_info->PINendosome);
daughter1->SetChemical(2,parent_info->PINendosome);
} else {
if (daughter2->AtBoundaryP() && !daughter1->AtBoundaryP()) {
//new_chem[2]=chem[2]=0.;
daughter1->SetNewChem(2,0);
daughter1->SetChemical(2,0);
/*new_chem[0]=chem[0]=0.;
for (list<Wall *>::const_iterator w=walls.begin();
w!=walls.end();
w++) {
(*w)->setTransporter(this, 1, 0.);
}*/
//daughter2->chem[2]=parent_info->PINendosome;
daughter2->SetChemical(2,parent_info->PINendosome);
//cerr << "Clearing parent\n";
} else {
//daughter1->new_chem[2]=daughter1->chem[2] = parent_info->PINendosome*(area/tot_area);
daughter1->SetNewChem(2,parent_info->PINendosome*(area/tot_area));
daughter1->SetChemical(2, parent_info->PINendosome*(area/tot_area));
//daughter2->new_chem[2]=daughter2->chem[2] = parent_info->PINendosome*(daughter_area/tot_area);
daughter2->SetNewChem(2,parent_info->PINendosome*(daughter_area/tot_area));
daughter2->SetChemical(2,parent_info->PINendosome*(daughter_area/tot_area));
}
}
/*
// NB: Code commented out; not yet adapted to plugin format... RM 18/12/2009
// Now redistribute the membrane PINs according to the original polarization in the parent
// mmm... I'd like to have a better, biologically motivated rule for this,
// but for lack of something better... I hope I'm excused :-). Let's say the overall
// organization of the actin fibres is not completely destroyed after division...
// distribute wallPINs according to the circumference of the parent and daughter
double circ = Circumference( );
double daughter_circ = daughter.Circumference();
double tot_circ = circ + daughter_circ;
double wallPINs = (circ / tot_circ) * parent_info->PINmembrane;
double daughter_wallPINs = (daughter_circ / tot_circ) * parent_info->PINmembrane;
//cerr << "wallPINs = " << wallPINs << ", daughter_wallPINs = " << daughter_wallPINs << "sum = " << wallPINs + daughter_wallPINs << ", PINmembrane = " << parent_info->PINmembrane << endl;
// distrubute it according to the overall polarity
Vector polarization = parent_info->polarization.Normalised().Perp2D();
double sum=0.;
for (list<Wall *>::const_iterator w=walls.begin();
w!=walls.end();
w++) {
// distribute according to angle (0 degrees: maximum, 180 degrees minimum)
double tmp=InnerProduct((*w)->getWallVector(this),polarization); // move domain from [-1,1] to [0,1]
cerr << "[" << tmp << "]";
sum+=tmp;
//(*w)->setTransporter(this, 1,
}
//cerr << "Sum is " << sum << endl;
//double sum_wall_Pi = SumTransporters(1);
// After division, cells produce PIN1 (in intracellular storage) until total amount becomes Pi_tot
//SetChemical(1, par.Pi_tot - sum_wall_Pi );
//SetNewChem(1, Chemical(1));
//cerr << "[ " << sum_wall_Pi + Chemical(1) << "]";
*/
}
void LeafPlugin::SetCellColor(CellBase *c, QColor *color) {
// Red: AUX1
// Green: Auxin
// Blue: van-3
// color->setRgb(chem[2]/(1+chem[2]) * 255.,(chem[0]/(1+chem[0]) * 255.),(chem[3]/(1+chem[3]) *255.) );
color->setRgb(c->Chemical(2)/(1+c->Chemical(2)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.),(c->Chemical(3)/(1+c->Chemical(3)) *255.) );
}
void LeafPlugin::CellHouseKeeping(CellBase *c) {
if (c->Boundary()==CellBase::None) {
if (c->Area() > par->rel_cell_div_threshold * c->BaseArea() ) {
//c->SetChemical(0,0);
c->Divide();
}
// expand if this is not a provascular cell
if (c->Chemical(3) < 0.7 ) {
c->EnlargeTargetArea(par->cell_expansion_rate);
}
}
}
void LeafPlugin::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
// leaf edge is const source of auxin
// (Neumann boundary condition: we specify the influx)
if (w->C2()->BoundaryPolP()) {
if (w->AuxinSource()) {
double aux_flux = par->leaf_tip_source * w->Length();
dchem_c1[0]+= aux_flux;
// dchem_c2 is undefined..!
return;
} else {
if (w->AuxinSink()) {
// efflux into Shoot Apical meristem
// we assume all PINs are directed towards shoot apical meristem
dchem_c1[0] -= par->sam_efflux * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0));
return;
} else {
// Active fluxes (PIN1 and AUX1 mediated transport)
// (Transporters measured in moles, here)
// efflux from cell 1 to cell 2
double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0))
+ par->aux1transport * w->C2()->Chemical(2) * w->C1()->Chemical(0) / (par->kaux1 + w->C1()->Chemical(0)) );
// efflux from cell 2 to cell 1
double trans21 = ( par->transport * w->Transporters2(1) * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0))
+ par->aux1transport * w->C1()->Chemical(2) * w->C2()->Chemical(0) / (par->kaux1 + w->C2()->Chemical(0)) );
dchem_c1[0] += trans21 - trans12;
dchem_c2[0] += trans12 - trans21;
return;
}
}
}
if (w->C1()->BoundaryPolP()) {
if (w->AuxinSource()) {
double aux_flux = par->leaf_tip_source * w->Length();
dchem_c2[0] += aux_flux;
// dchem_c1 is undefined...!
return;
} else {
if (w->AuxinSink()) {
// efflux into Shoot Apical meristem
// we assume all PINs are directed towards shoot apical meristem
// no passive fluxes: outside is impermeable
// Active fluxes (PIN1 and AUX1 mediated transport)
// (Transporters measured in moles, here)
// efflux from cell 1 to cell 2
// assumption: no AUX1 in shoot apical meristem
double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0)));
dchem_c1[0] += - trans12;
return;
//dchem_c2[0] -= par->sam_efflux * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0));
// return;
} else {
}
}
}
// Passive fluxes (Fick's law)
// only auxin flux now
// flux depends on edge length and concentration difference
for (int c=0;c<NChem();c++) {
double phi = w->Length() * ( par->D[c] ) * ( w->C2()->Chemical(c) - w->C1()->Chemical(c) );
dchem_c1[c] += phi;
dchem_c2[c] -= phi;
}
// Active fluxes (PIN1 and AUX1 mediated transport)
// (Transporters measured in moles, here)
// efflux from cell 1 to cell 2
double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0))
+ par->aux1transport * w->C2()->Chemical(2) * w->C1()->Chemical(0) / (par->kaux1 + w->C1()->Chemical(0)) );
// efflux from cell 2 to cell 1
double trans21 = ( par->transport * w->Transporters2(1) * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0))
+ par->aux1transport * w->C1()->Chemical(2) * w->C2()->Chemical(0) / (par->kaux1 + w->C2()->Chemical(0)) );
dchem_c1[0] += trans21 - trans12;
dchem_c2[0] += trans12 - trans21;
}
void LeafPlugin::WallDynamics(Wall *w, double *dw1, double *dw2) {
// Cells polarize available PIN1 to Shoot Apical Meristem
if (w->C2()->BoundaryPolP()) {
if (w->AuxinSink()) {
dw1[0] = 0.; dw2[0] = 0.;
dw1[2] = 0.; dw2[2] = 0.;
// assume high auxin concentration in SAM, to convince PIN1 to polarize to it
// exocytosis regulated0
double nb_auxin = par->sam_auxin;
double receptor_level = nb_auxin * par->r / (par->kr + nb_auxin);
dw1[1] = par->k1 * w->C1()->Chemical(1) * receptor_level /( par->km + w->C1()->Chemical(1) ) - par->k2 * w->Transporters1(1);
dw2[1] = 0.;
return;
} else {
dw1[0]=dw2[0]=dw1[1]=dw2[1]=dw1[2]=dw2[2];
return;
}
}
if (w->C1()->BoundaryPolP()) {
if (w->AuxinSink()) {
dw1[0] = 0.; dw2[0] = 0.;
dw1[2] = 0.; dw2[2] = 0.;
// assume high auxin concentration in SAM, to convince PIN1 to polarize to it
// exocytosis regulated
double nb_auxin = par->sam_auxin;
double receptor_level = nb_auxin * par->r / (par->kr + nb_auxin);
dw2[1] = par->k1 * w->C2()->Chemical(1) * receptor_level /( par->km + w->C2()->Chemical(1) ) - par->k2 * w->Transporters2(1);
dw1[1] = 0.;
return;
} else {
dw1[0]=dw2[0]=dw1[1]=dw2[1]=dw1[2]=dw2[2];
return;
}
}
// PIN1 localization at wall 1
// Note: chemical 0 is Auxin (intracellular storage only)
// Chemical 1 is PIN1 (walls and intracellular storage)
//! \f$ \frac{d Pij/dt}{dt} = k_1 A_j \frac{P_i}{L_ij} - k_2 P_{ij} \f$
// Note that Pij is measured in term of concentration (mol/L)
// Pi in terms of quantity (mol)
double dPijdt1=0., dPijdt2=0.;
// normal cell
double auxin2 = w->C2()->Chemical(0);
double receptor_level1 = auxin2 * par->r / (par->kr + auxin2);
dPijdt1 =
// exocytosis regulated
par->k1 * w->C1()->Chemical(1) * receptor_level1 / ( par->km + w->C1()->Chemical(1) ) - par->k2 * w->Transporters1(1);
double auxin1 = w->C1()->Chemical(0);
double receptor_level2 = auxin1 * par->r / (par->kr + auxin1);
// normal cell
dPijdt2 =
// exocytosis regulated
par->k1 * w->C2()->Chemical(1) * receptor_level2 / ( par->km + w->C2()->Chemical(1) ) - par->k2 * w->Transporters2(1);
/* PIN1 of neighboring vascular cell inhibits PIN1 endocytosis */
dw1[0] = 0.; dw2[0] = 0.;
dw1[2] = 0.; dw2[2] = 0.;
dw1[1] = dPijdt1;
dw2[1] = dPijdt2;
}
double LeafPlugin::complex_PijAj(CellBase *here, CellBase *nb, Wall *w) {
// gives the amount of complex "auxinreceptor-Pin1" at the wall (at QSS)
//return here.Chemical(1) * nb.Chemical(0) / ( par->km + here.Chemical(1));
double nb_aux = (nb->BoundaryPolP() && w->AuxinSink()) ? par->sam_auxin : nb->Chemical(0);
double receptor_level = nb_aux * par->r / (par->kr + nb_aux);
return here->Chemical(1) * receptor_level / ( par->km + here->Chemical(1));
}
void LeafPlugin::CellDynamics(CellBase *c, double *dchem) {
double dPidt = 0.;
double sum_Pij = c->SumTransporters( 1 );
// exocytosis regulated:
// van3 expression reduces rate of PIN1 endocytosis
dPidt = -par->k1 * c->ReduceCellAndWalls<double>( far_3_arg_mem_fun( *this, &LeafPlugin::complex_PijAj ) ) +
(c->Chemical(3) < 0.5 ? par->k2 : par->k2van3) * sum_Pij;
// production of PIN depends on auxin concentration
dPidt += (c->AtBoundaryP()?par->pin_prod_in_epidermis:par->pin_prod) * c->Chemical(0) - c->Chemical(1) * par->pin_breakdown;
/*if (c->AtBoundaryP()) {
dchem[2] = 0.01;
//cerr << "Making cell blue.\n";
} else {
dchem[2] = -0.1 * c->Chemical(2);
}*/
// no PIN production in SAM
if (c->Boundary() == CellBase::SAM) {
dchem[1]=0.;
dchem[0]= - par->sam_auxin_breakdown * c->Chemical(0);
dchem[2]=0.;
} else {
dchem[1] = dPidt;
// source of auxin
dchem[0] = par->aux_cons;
// auxin-induced AUX1 production, in the epidermis
dchem[2] = ( c->AtBoundaryP() ? par->aux1prod : par->aux1prodmeso ) * ( c->Chemical(0) / ( 1. + par->kap * c->Chemical(0) ) ) - ( par->aux1decay ) * c->Chemical(2) ;//: 0.;
// auxin-induced production of VAN-3? Autokatalysis?
//dchem[3] = par->van3prod * (c->Chemical(0) / (1. + par->kvp * c-> Chemical(0) ) )
double A = c->Chemical(0);
double van3 = c->Chemical(3);
dchem[3] = par->van3prod * A - par->van3autokat * van3 + van3*van3/(1 + par->van3sat * van3*van3 );
}
}
Q_EXPORT_PLUGIN2(leafplugin, LeafPlugin)
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