PINFlux.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 "PINFlux.h"

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

#include <functional>
using namespace std;
using boost::property_tree::ptree;

namespace SimPT_Default {
namespace CellChemistry {

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

void PINFlux::Initialize(const CoreData& cd)
{
        m_cd = cd;
        const auto& p = m_cd.m_parameters->get_child("auxin_transport");

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

void PINFlux::operator()(Cell* cell, double* dchem)
{
        // sum all incoming fluxes of PINs
        dchem[1] = -SumFluxFromWalls(cell);
}

double PINFlux::SumFluxFromWalls(Cell* cell)
{
        using std::placeholders::_1;
        using std::placeholders::_2;
        using std::placeholders::_3;

        function<double(Cell*, Cell*, Wall*)> f = bind(&PINFlux::Flux, this, _1, _2, _3);
        double const sum = ReduceCellWalls<double>(cell, f);
        return sum;
}

double PINFlux::Flux(Cell* this_cell, Cell* adjacent_cell, Wall* w)
{
        // PIN1 localization at wall
        // Note: chemical 0 is Auxin (intracellular storage only)
        //  PIN1 is Chemical 1 (both in walls and intracellular storage)
        // Note that Pij is measured in term of concentration (mol/L)
        // Pi in terms of quantity (mol)
        // Equations as in Merks et al., Trends in Plant Science 2007

        // calculate PIN translocation rate from cell to membrane
        double const adj_auxin = adjacent_cell->GetChemical(0);
        double const receptor = adj_auxin * m_r / (m_kr + adj_auxin);

        // pick the correct side of the Wall
        double pin_atwall;
        if (w->GetC1() == this_cell) {
                pin_atwall = w->GetTransporters1(1);
        } else {
                pin_atwall = w->GetTransporters2(1);
        }

        // note: pin_flux is net flux from endosome to wall
        double const chem = this_cell->GetChemical(1);
        double const pin_flux = m_k1 * chem * receptor / (m_km + chem) - m_k2 * pin_atwall;
        return pin_flux;
}

} // namespace
} // namespace