---

Geometry.cpp

Go to the documentation of this file.

// Geometry.cpp: implementation of the CGeometry class.
//

#include <math.h>
#include "Cell.h"
#include "Display.h"
#include "DNA.h"
#include "Components.h"
#include "Geometry.h"

// Construction/Destruction
CGeometry::CGeometry(CCell *pCell)
{
        m_pCell=pCell;
        SL[0]=0;                //Septum length
        SL[1]=0;
        SL[2]=0;
        CW = 0.75E-4;   //Cell Width
        CL = 1.52E-4;   //Cell Length
        DEN = 0.282;            //Density
        S = 3.6E-08;                    //Cellular Surface Area
        V = 5.65E-13;                   //Volume
        SEPF[0] = 0.0;
        SEPF[1] = 0.0;
        SEPF[2]=0.0;    //Area of each septum
        NSEPF = 0;              //number of septa
        CSL[0] = 0.0;
        CSL[1]=0.0;
        CSL[2]=0.0;//unit change 10000*(septum length)
        E2=5.62E-4*V;   //initialize E2
        E3[0]=0;
        E3[1]=0;
        E3[2]=0;
        double E3TOT = 0.0;     //declare E3TOT
        for(int i=0; i<3; i++)
                E3TOT = E3TOT + E3[i];  //Add total (doesn't really change anything)
        E23 = E3TOT + E2;       //total cell envelope enzymes
}

CGeometry::CGeometry()
{

}

CGeometry::~CGeometry()
{

}


CGeometry::CGeometry(const CGeometry &rGeom, CCell *pCell)
{
        //*this=*rGeom;
        m_pCell=pCell;
}

double CGeometry::GetVolume()
{
        return V;
}

//This function checks volume to insure that it is consistent with mass and density
void CGeometry::CheckVolume()
{
        double VB=V;                                                                    //Initial volume placeholder
        ComputeVolume();                                                                        //Calculate total volume based on mass
        if(fabs((VB-V)/V) > 0.1)                                                //Volume and mass disagree by > 10%
                m_pCell->GetDisplay()->WarningMessage(1);       //Mismatch warning
        return;
}

void CGeometry::ComputeVolume()
{
        double TotalMass=0.0;                                                   //Total cell mass
        for(int i=0;i<11;i++)
                TotalMass+=m_pCell->GetComponents()->GetY(i);   //Add up total mass
        double MassEnv=m_pCell->GetComponents()->GetY(9);       //Envelope mass
        double VE = MassEnv/0.42/0.5526;                                        //Envelope volume
        double VC = (TotalMass-MassEnv/0.42)/0.2584;                    //Cytoplasm volume
        V=VC+VE;                        
}

void CGeometry::UpdateShape()
{

        if(m_pCell->GetDNA()->CheckTerm())                                              //if termination occured, add septa
                AddSepta();
        E2=m_pCell->GetComponents()->GetY(12);
        double E3TOT=0.0;
        for(int i=0;i<3;++i)
                E3TOT += E3[i]*(pow(2,i));      //Calculate total cross wall enzyme
        E23=E2+E3TOT;                           //total (E2+E3) env. enzymes

        double PRCNT=E2/E23;                            //% of total envelope enzymes
        double PRCNTS[3];
        for(i=0;i<3;++i)
                PRCNTS[i] = E3[i]/E23;  //% of total envelope enzymes
        double DS=(1.2E6/0.42)*m_pCell->GetComponents()->GetDY9()*m_pCell->GetComponents()->DT; //relates change in surface area
                                                                        //area to rate of cell envelope synthesis
        double SEPFTOT=0.0;
        for(i=0;i<3;++i)
        {
                SEPF[i] += PRCNTS[i]*DS;        //area of each septa
                SEPFTOT += SEPF[i]*(pow(2,i));  //total septa area
        }

        double DCL = (PRCNT*DS)/(3.14*CW);      //change in cell length
        CL+=DCL;                                                //adjust cell length accordingly
        S+=DS;                                                  //calculate surface area
        CW=CalcWidth();                 //call width function
        CL=S/(3.14159*CW)-CW-2.0*SL[0]-4.0*SL[1]-8.0*SL[2];     
                                                                //recalculate cell length
        double CN=CW*1.0E4;                             //cell width unit change
        double CM=(CL+2.0*SL[0]+4.0*SL[1]+8.0*SL[2]+CW)*1.0E4;
                                                                        //total cell length
        for(i=0;i<3;++i)
                CSL[i]=SL[i]*1.0E4;                     //septum length unit change
}

void CGeometry::AddSepta()
{
        if(NSEPF<3)             //limit number of septa
        {
                ++NSEPF;                //add a septa
        }
        double Y13=m_pCell->GetComponents()->GetY(13);
        E3[NSEPF-1]=Y13/pow(2,(NSEPF-1));       //divide enzyme among septa
        m_pCell->GetComponents()->ResetY(13);
}

double CGeometry::GetWidth()
{
        return CW;
}

double CGeometry::CalcWidth()
{
        int i=0;
        //Newton's method
        for(i=0;i<100;++i)
        {
                double FS=0.0;
                double DFS=0.0;
                for(int j=0;j<3;++j)
                {
                        SL[j]=SEPF[j]/(2*3.14159*CW);
                        DFS += (pow(0.25,(j+1))*pow(SEPF[j],3));
                        FS += (pow(2,(j+1))*pow(SL[j],3));
                }
                double F = -.262*pow(CW,3)+0.25*S*CW-1.047*FS-V;
                double DF = -0.7854*pow(CW,2)+0.25*S+0.1013*DFS/pow(CW,4);
                double CWN=CW-F/DF;
                if((fabs(F)<=0.001)&&(fabs((CW-CWN)/CWN)<=0.001))
                {
                        CW=CWN;
                        break;
                }
                CW=CWN;                         //set new guess and continue with iteration
        }
        for(int j=0;j<3;++j)
                SL[j]=SEPF[j]/(2*3.14159*CW);   //compute septa lengths
        
        if(i<5)
                return CW;

        m_pCell->GetDisplay()->WarningMessage(2);
        return CW;
}

double CGeometry::GetSurface()
{
        return S;
}

double CGeometry::GetSepf()
{
        return SEPF[0];
}

void CGeometry::Divide()
{
        SEPF[0]=SEPF[1];
        SEPF[1]=SEPF[2];
        SEPF[2]=0.0;            //Shift septa indeces
        S=0.5*S;                        //1/2 the surface area
        V=0.5*V;                        //1/2 the volume
        CL=0.5*CL;                      //half the cell length
        E2=0.5*E2;                      //half E2
        E3[0]=E3[1];            
        E3[1]=E3[2];
        E3[2]=0.0;                      //Shift septa enzyme indeces
        NSEPF=NSEPF-1;  //1 less septa to worry about
}

---