cell2cell_transport/Source.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 "Source.h"

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

namespace SimPT_Default {
namespace CellToCellTransport {

using namespace std;
using namespace boost::property_tree;

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

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

        m_chemical_count    = p->get<unsigned int>("model.cell_chemical_count");
        m_ka                = p->get<double>("auxin_transport.ka");
        m_tip_source   = p->get<double>("auxin_transport.leaf_tip_source");
        m_transport         = p->get<double>("auxin_transport.transport");

        m_D.assign(m_chemical_count, 0.0);
        boost::optional<ptree&> arr_D = p->get_child_optional("auxin_transport.D.value_array");
        if (arr_D) {
                m_D[0] = arr_D->begin()->second.get_value<double>();
        }
}

void Source::operator()(Wall* w, double* dchem_c1, double* dchem_c2)
{
        double const phi = w->GetLength() * m_D[0]
                                * (w->GetC2()->GetChemical(0) - w->GetC1()->GetChemical(0));
        dchem_c1[0] += phi;
        dchem_c2[0] -= phi;

        // Active fluxes (PIN1 mediated transport)(Transporters measured in moles, here)
        double const trans12 = m_transport * w->GetTransporters1(1) * w->GetC1()->GetChemical(0)
                                        / (m_ka + w->GetC1()->GetChemical(0));
        double const trans21 = m_transport * w->GetTransporters2(1) * w->GetC2()->GetChemical(0)
                                        / (m_ka + w->GetC2()->GetChemical(0));

        dchem_c1[0] += trans21 - trans12;
        dchem_c2[0] += trans12 - trans21;

        // Influx at leaf "AuxinSource" (as specified in initial condition)
        if (w->IsAuxinSource()) {
                double const aux_flux = m_tip_source * w->GetLength();
                dchem_c1[0] += aux_flux;
                dchem_c2[0] += aux_flux;
        }
}

} // namespace
} // namespace