wall_chemistry/AuxinGrowth.cpp

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/*
 * Copyright 2011-2016 Universiteit Antwerpen
 *
 * Licensed under the EUPL, Version 1.1 or  as soon they will be approved by
 * the European Commission - subsequent versions of the EUPL (the "Licence");
 * You may not use this work except in compliance with the Licence.
 * You may obtain a copy of the Licence at: http://ec.europa.eu/idabc/eupl5
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the Licence is distributed on an "AS IS" basis,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the Licence for the specific language governing
 * permissions and limitations under the Licence.
 */
#include "AuxinGrowth.h"

#include "bio/Cell.h"
#include "bio/Wall.h"

namespace SimPT_Default {
namespace WallChemistry {

using namespace std;
using namespace boost::property_tree;

AuxinGrowth::AuxinGrowth()
        : m_k1(0.0), m_k2(0.0), m_km(0.0), m_kr(0.0), m_r(0.0), m_sam_auxin(0.0)
{
}

AuxinGrowth::AuxinGrowth(const CoreData& cd)
        : AuxinGrowth()
{
        Initialize(cd);
}

void AuxinGrowth::Initialize(const CoreData& cd)
{
        m_cd = cd;
                auto& p = m_cd.m_parameters;

                m_k1        = p->get<double>("auxin_transport.k1");
                m_k2        = p->get<double>("auxin_transport.k2");
                m_km        = p->get<double>("auxin_transport.km");
                m_kr        = p->get<double>("auxin_transport.kr");
                m_r         = p->get<double>("auxin_transport.r");
                m_sam_auxin = p->get<double>("auxin_transport.sam_auxin");
}

void AuxinGrowth::operator()(Wall* w, double* dw1, double* dw2)
{
        // Cells polarize available PIN1 to Shoot Apical Meristem
        if (w->GetC2()->IsBoundaryPolygon()) {
                if (w->IsAuxinSink()) {
                        dw1[0] = 0.;
                        dw2[0] = 0.;

                        // assume high auxin concentration in SAM, to convince PIN1 to polarize to it
                        // exocytosis regulated
                        double const chem = w->GetC1()->GetChemical(1);
                        double const receptor = m_sam_auxin * m_r / (m_kr + m_sam_auxin);
                        dw1[1] = m_k1 * chem * receptor / (m_km + chem)
                                                        - m_k2 * w->GetTransporters1(1);
                        dw2[1] = 0.;
                } else {
                        dw1[0] = dw2[0] = dw1[1] = dw2[1];
                }
                return;
        }

        if (w->GetC1()->IsBoundaryPolygon()) {
                if (w->IsAuxinSink()) {
                        dw1[0] = 0.;
                        dw2[0] = 0.;

                        // assume high auxin concentration in SAM, to convince PIN1 to polarize to it
                        // exocytosis regulated
                        double const chem = w->GetC2()->GetChemical(1);
                        double const receptor = m_sam_auxin * m_r / (m_kr + m_sam_auxin);
                        dw1[1] = 0.;
                        dw2[1] = m_k1 * chem * receptor / (m_km + chem)
                                                        - m_k2 * w->GetTransporters2(1);
                } else {
                        dw1[0] = dw2[0] = dw1[1] = dw2[1];
                }
                return;
        }

        // PIN1 localization at wall 1
        // Chemical 0 is Auxin (intracellular storage only)
        // Chemical 1 is PIN1  (walls and intracellular storage)
        // Note: Pij measured in terms of concentration (mol/L); Pi in terms of quantity (mol)

        // normal cell -- exocytosis regulated
        double const auxin2     = w->GetC2()->GetChemical(0);
        double const chem_1_1   = w->GetC1()->GetChemical(1);
        double const receptor1  = auxin2 * m_r / (m_kr + auxin2);
        double const dPijdt1    = m_k1 * chem_1_1 * receptor1 / (m_km + chem_1_1)
                                                        - m_k2 * w->GetTransporters1(1);

        // normal cell -- exocytosis regulated
        double const auxin1     = w->GetC1()->GetChemical(0);
        double const chem_2_1   = w->GetC2()->GetChemical(1);
        double const receptor2  = auxin1 * m_r / (m_kr + auxin1);
        double const dPijdt2    = m_k1 * chem_2_1 * receptor2 / (m_km + chem_2_1)
                                                        - m_k2 * w->GetTransporters2(1);

        // PIN1 of neighboring vascular cell inhibits PIN1 endocytosis
        dw1[0] = 0.;
        dw2[0] = 0.;
        dw1[1] = dPijdt1;
        dw2[1] = dPijdt2;
}

} // namespace
} // namespace