/*******************************************************************
  psim.cpp

  Revision 1.2

  under construction

********************************************************************/
/* Copyright (C) 2000,2001  Doug Neubauer
*
* This program 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.
*
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
*/


#define  MILLISECONDSPERHOUR    (3600000)


// double  stomachPeptides = 0.0;

#include <stdlib.h>
#include <stdio.h>
#include <math.h>                         
#include <string.h>
#include <time.h>
#include <conio.h>
#include "psim.h"

/* begin physiological data */


                                 
tissueConstant tissueConstants[] = {
{"lymphNode",
 {3.0e8 * 0.52 ,   3.0e8 * 0.52 * STRAINFREQUENCY ,   3.0e8 * 0.52 * STRAINFREQUENCY },      /* numberOfBCellsNaive  */
 {3.0e8 * 0.48 ,  3.0e8 * 0.48 * STRAINFREQUENCY  ,  3.0e8 * 0.48 * STRAINFREQUENCY },      /* numberOfBCellsRecirculate  */
 {0.0 ,           0.0         },      /* numberOfBCellsMarginalZone  */
 {7.0e8 * 0.9,    7.0e8 * 0.9 * STRAINFREQUENCY,    7.0e8 * 0.9 * STRAINFREQUENCY },      /* numberOfThCellsNaive  */
 {7.0e8 * 0.9,    7.0e8 * 0.9 * STRAINFREQUENCY,    7.0e8 * 0.9 * STRAINFREQUENCY },      /* numberOfTcCellsNaive  */
  3.5e6,                      /* numberOfMacrophage  */
  3.2e7,                      /* numberOfDendritic  */
  0.0,                        /* epitheliaCell  */
  1.15,                       /* k2BloodInput_bCellNaive  */
  0.24,                       /* k2BloodInput_bCellNaiveRecirculate  */
  0.35,                       /* k2BloodInput_thNaive  */
  0.21,                       /* k2BloodInput_tcNaive  */
  0.0,                 /* k2BloodInput_tcEffector  */
  0.0,                        /* k2BloodInput_Dendritic  */
  0.0,                        /* k2BloodInput_rbc  */
  0.0 ,                       /* k2BloodInput_platelets  */
  0.0 ,                       /* k2BloodInput_Macrophage  */
  0.0 ,                       /* k2BloodOutput_bCellNaive */
  0.0 ,                       /* k2BloodOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodOutput_thNaive  */
  0.0 ,                       /* k2BloodOutput_tcNaive  */
  0.05 ,                      /* k2LymphInput_bCellNaiveRecirculate  */
  0.05 ,                      /* k2LymphInput_macrophageApc  */
  0.05 ,                      /* k2LymphInput_dendriticApc  */
  23.0 * 24.0 ,               /* k2LymphOutput_bCellNaiveRecirculate  */
  0.05 ,                       /* k2LymphOutput_tcEffectorfector  */
  0.0 ,                       /* k2LymphOutput_macrophageApc  */
  0.0 ,                       /* k2LymphOutput_dendriticApc  */
  16.3 * 24.0 ,               /* k2LymphOutput_thNaive  */
  54.7 * 24.0 ,               /* k2LymphOutput_tcNaive  */
  0.0 ,                       /* k2macrophageReplicate  */
  0.0 ,                       /* k2dendriticReplicate  */
  0.0,                        /* k2BloodInput_plasmaCell  */
  0.05 ,                       /* k2LymphOutput_plasmaCell  */
  0.0,                         /* k2BloodInput_thEffector  */                                           
  0.05 ,                       /* k2LymphOutput_thEffectorfector  */
  2000.0 ,                       /* fdcGerminalCenters  */
   0.0,                        /* k2BloodInput_bCellMemory */   
   0.0,                        /* k2BloodInput_thMemory */      
   0.0,                        /* k2BloodInput_tcMemory */      
   0.0,                        /* k2BloodOutput_bCellMemory */  
   0.0,                        /* k2BloodOutput_thMemory */     
   0.0,                        /* k2BloodOutput_tcMemory */     
   23.0 * 24.0 ,                       /* k2LymphOutput_bCellMemory ul/sec */  
   23.0 * 24.0 ,                       /* k2LymphOutput_thMemory */     
   23.0 * 24.0 ,                       /* k2LymphOutput_tcMemory */     
   0.05,                        /* k2LymphInput_bCellMemory */   
   0.05,                        /* k2LymphInput_thMemory */      
   0.05,                        /* k2LymphInput_tcMemory */      
   0.0,                        /* numberOfmastCell        */  
   0.0,                        /* numberOfeosinophil      */  
   0.0,                        /* k2BloodInput_mastCell   */  
   0.0,                        /* k2BloodInput_eosinophil */  
 },
{"spleen",
 {3.5e10 * 0.5 * 0.7 / 3.5, 3.5e10 * 0.5 * 0.7 / 3.5 * STRAINFREQUENCY,3.5e10 * 0.5 * 0.7 / 3.5 * STRAINFREQUENCY},   /* numberOfBCellsNaive  */
 {3.5e10 * 1.3 / 3.5 ,      3.5e10 * 1.3 / 3.5       * STRAINFREQUENCY,3.5e10 * 1.3 / 3.5       * STRAINFREQUENCY},   /* numberOfBCellsRecirculate  */
 {3.5e10 * 1.5 / 3.5,       3.5e10 * 1.5 / 3.5       * STRAINFREQUENCY,3.5e10 * 1.5 / 3.5       * STRAINFREQUENCY},   /* numberOfBCellsMarginalZone  */
 {2.73e10 * 0.69,           2.73e10 * 0.69           * STRAINFREQUENCY,2.73e10 * 0.69           * STRAINFREQUENCY},   /* numberOfThCellsNaive  */
 {7.7e9,                    7.7e9                    * STRAINFREQUENCY,7.7e9                    * STRAINFREQUENCY},   /* numberOfTcCellsNaive  */
  4.6e10,                              /* numberOfMacrophage  */
  0.0 ,                               /* numberOfDendritic  */
  0.0 ,                          /* epitheliaCell  */
  1151.0 ,                       /* k2BloodInput_bCellNaive  */
  1151.0 ,                       /* k2BloodInput_bCellNaiveRecirculate  */
  1151.0 ,                       /* k2BloodInput_thNaive  */
  1151.0,                        /* k2BloodInput_tcNaive  */
  0.0,                 /* k2BloodInput_tcEffector  */
  0.0,                        /* k2BloodInput_Dendritic  */
  0.36,                        /* k2BloodInput_rbc  */
  6.84 ,                       /* k2BloodInput_platelets  */
  24.0 ,                       /* k2BloodInput_Macrophage  */
  1.5 ,                       /* k2BloodOutput_bCellNaive */
  11.7 ,                       /* k2BloodOutput_bCellNaiveRecirculate  */
  2.5 ,                       /* k2BloodOutput_thNaive  */
  2.1 ,                       /* k2BloodOutput_tcNaive  */
  0.0 ,                       /* k2LymphInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphInput_macrophageApc  */
  0.0 ,                       /* k2LymphInput_dendriticApc  */
  0.0 ,                       /* k2LymphOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphOutput_tcEffector  */
  0.0 ,                       /* k2LymphOutput_macrophageApc  */
  0.0 ,                       /* k2LymphOutput_dendriticApc  */
  0.0 ,                       /* k2LymphOutput_thNaive  */
  0.0 ,                       /* k2LymphOutput_tcNaive  */
  4.0 * 24.0 ,              /* k2macrophageReplicate  */
  0.0 ,                       /* k2dendriticReplicate  */
  0.0,                        /* k2BloodInput_plasmaCell  */
  0.0 ,                       /* k2LymphOutput_plasmaCell  */
  0.0,                         /* k2BloodInput_thEffector  */
  0.0 ,                       /* k2LymphOutput_thEffectorfector  */
  75000.0 ,                       /* fdcGerminalCenters  */
   1151.0,                        /* k2BloodInput_bCellMemory */   
   1151.0,                        /* k2BloodInput_thMemory */      
   1151.0,                        /* k2BloodInput_tcMemory */      
   2.5,                        /* k2BloodOutput_bCellMemory */  
   2.5,                        /* k2BloodOutput_thMemory */     
   2.5,                        /* k2BloodOutput_tcMemory */     
   0.0,                                /* k2LymphOutput_bCellMemory */  
   0.0,                                /* k2LymphOutput_thMemory */     
   0.0,                                /* k2LymphOutput_tcMemory */     
   0.0,                         /* k2LymphInput_bCellMemory */   
   0.0,                         /* k2LymphInput_thMemory */      
   0.0,                         /* k2LymphInput_tcMemory */      
   0.0,                        /* numberOfmastCell        */  
   0.0,                        /* numberOfeosinophil      */  
   0.0,                        /* k2BloodInput_mastCell   */  
   0.0,                        /* k2BloodInput_eosinophil */  
 },
{"liver",
 {0.0,      0.0  * STRAINFREQUENCY, 0.0  * STRAINFREQUENCY},            /* numberOfBCellsNaive  */
 {1.6e8 ,  1.6e8 * STRAINFREQUENCY,1.6e8 * STRAINFREQUENCY},            /* numberOfBCellsRecirculate  */
 {0.0,      0.0  * STRAINFREQUENCY, 0.0  * STRAINFREQUENCY},            /* numberOfBCellsMarginalZone  */
 {4.0e8,   4.0e8 * STRAINFREQUENCY,4.0e8 * STRAINFREQUENCY},            /* numberOfThCellsNaive  */
 {5.6e8,   5.6e8 * STRAINFREQUENCY,5.6e8 * STRAINFREQUENCY},            /* numberOfTcCellsNaive  */
  1.0e11,                     /* numberOfMacrophage  */
  0.0 ,                       /* numberOfDendritic  */
  0.0 ,                       /* epitheliaCell  */
  0.0 ,                       /* k2BloodInput_bCellNaive  */
  1.61e-2 * 77.0,             /* k2BloodInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodInput_thNaive  */
  0.0,                        /* k2BloodInput_tcNaive  */
  5.2,                 /* k2BloodInput_tcEffector  */
  0.0,                        /* k2BloodInput_Dendritic  */
  0.0,                        /* k2BloodInput_rbc  */
  0.0 ,                       /* k2BloodInput_platelets  */
  50.0 ,                      /* k2BloodInput_Macrophage  */
  0.0 ,                       /* k2BloodOutput_bCellNaive */
  0.0 ,                       /* k2BloodOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodOutput_thNaive  */
  0.0 ,                       /* k2BloodOutput_tcNaive  */
  0.0 ,                       /* k2LymphInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphInput_macrophageApc  */
  0.0 ,                       /* k2LymphInput_dendriticApc  */
  5.6 * 24.0 ,                /* k2LymphOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphOutput_tcEffector  */
  0.0 ,                       /* k2LymphOutput_macrophageApc  */
  0.0 ,                       /* k2LymphOutput_dendriticApc  */
  0.0 ,                       /* k2LymphOutput_thNaive  */
  0.0 ,                       /* k2LymphOutput_tcNaive  */
  0.0 ,                       /* k2macrophageReplicate  */
  0.0 ,                       /* k2dendriticReplicate  */
  5.2,                        /* k2BloodInput_plasmaCell  */
  0.0 ,                       /* k2LymphOutput_plasmaCell  */
  5.2,                         /* k2BloodInput_thEffector  */
  0.0 ,                       /* k2LymphOutput_thEffectorfector  */
  0.0 ,                       /* fdcGerminalCenters  */
   5.2,                        /* k2BloodInput_bCellMemory */   
   5.2,                        /* k2BloodInput_thMemory */      
   5.2,                        /* k2BloodInput_tcMemory */      
   0.0,                        /* k2BloodOutput_bCellMemory */  
   0.0,                        /* k2BloodOutput_thMemory */     
   0.0,                        /* k2BloodOutput_tcMemory */     
   4.0 * 24.0,                         /* k2LymphOutput_bCellMemory */  
   4.0 * 24.0,                         /* k2LymphOutput_thMemory */     
   4.0 * 24.0,                         /* k2LymphOutput_tcMemory */     
   0.0,                         /* k2LymphInput_bCellMemory */   
   0.0,                         /* k2LymphInput_thMemory */      
   0.0,                         /* k2LymphInput_tcMemory */      
   0.0,                        /* numberOfmastCell        */  
   0.0,                        /* numberOfeosinophil      */  
   0.0,                        /* k2BloodInput_mastCell   */  
   0.0,                        /* k2BloodInput_eosinophil */  
 },
{"skin",
 {0.0,      0.0                   , 0.0                    },                     /* numberOfBCellsNaive  */
 {8.0e6 ,  8.0e6 * STRAINFREQUENCY,8.0e6 * STRAINFREQUENCY  },            /* numberOfBCellsRecirculate  */
 {0.0  ,   0.0                    ,0.0                      },                          /* numberOfBCellsMarginalZone  */
 {3.6e8,   3.6e8 * STRAINFREQUENCY,3.6e8 * STRAINFREQUENCY},            /* numberOfThCellsNaive  */
 {3.6e8,   3.6e8 * STRAINFREQUENCY,3.6e8 * STRAINFREQUENCY},            /* numberOfTcCellsNaive  */
  0.0,                        /* numberOfMacrophage  */
  1.0e9 ,                       /* numberOfDendritic  */
  0.0 ,                       /* epitheliaCell  */
  0.0 ,                       /* k2BloodInput_bCellNaive  */
  1.61e-2 * 7.0,              /* k2BloodInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodInput_thNaive  */
  0.0,                        /* k2BloodInput_tcNaive  */
  3.5,                 /* k2BloodInput_tcEffector  */
  0.0,                        /* k2BloodInput_Dendritic  */
  0.0,                        /* k2BloodInput_rbc  */
  0.0 ,                       /* k2BloodInput_platelets  */
  0.0 ,                       /* k2BloodInput_Macrophage  */
  0.0 ,                       /* k2BloodOutput_bCellNaive */
  0.0 ,                       /* k2BloodOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodOutput_thNaive  */
  0.0 ,                       /* k2BloodOutput_tcNaive  */
  0.0 ,                       /* k2LymphInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphInput_macrophageApc  */
  0.0 ,                       /* k2LymphInput_dendriticApc  */
  3.1 * 24.0 ,                /* k2LymphOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphOutput_tcEffector  */
  0.0 ,                       /* k2LymphOutput_macrophageApc  */
  0.0 ,                       /* k2LymphOutput_dendriticApc  */
  0.0 ,                       /* k2LymphOutput_thNaive  */
  0.0 ,                       /* k2LymphOutput_tcNaive  */
  0.0 ,                       /* k2macrophageReplicate  */
  0.0 ,                       /* k2dendriticReplicate  */
  3.5,                        /* k2BloodInput_plasmaCell  */
  0.0 ,                       /* k2LymphOutput_plasmaCell  */
  3.5,                         /* k2BloodInput_thEffector  */
  0.0 ,                       /* k2LymphOutput_thEffectorfector  */
  0.0 ,                       /* fdcGerminalCenters  */
   3.5,                        /* k2BloodInput_bCellMemory */   
   3.5,                        /* k2BloodInput_thMemory */      
   3.5,                        /* k2BloodInput_tcMemory */      
   0.0,                        /* k2BloodOutput_bCellMemory */  
   0.0,                        /* k2BloodOutput_thMemory */     
   0.0,                        /* k2BloodOutput_tcMemory */     
   4.0 * 24.0,                          /* k2LymphOutput_bCellMemory */  
   4.0 * 24.0,                         /* k2LymphOutput_thMemory */     
   4.0 * 24.0,                         /* k2LymphOutput_tcMemory */     
   0.0,                         /* k2LymphInput_bCellMemory */   
   0.0,                         /* k2LymphInput_thMemory */      
   0.0,                         /* k2LymphInput_tcMemory */      
   0.0,                        /* numberOfmastCell        */  
   0.0,                        /* numberOfeosinophil      */  
   0.0,                        /* k2BloodInput_mastCell   */  
   0.0,                        /* k2BloodInput_eosinophil */  
 },
{"miscellaneousTissue",
 {0.0,      0.0                   ,  0.0                    },            /* numberOfBCellsNaive  */
 {2.0e10 ,2.0e10 * STRAINFREQUENCY,2.0e10 * STRAINFREQUENCY },            /* numberOfBCellsRecirculate  */
 {0.0,     0.0                    , 0.0                     },            /* numberOfBCellsMarginalZone  */
 {1.0e10, 1.0e10 * STRAINFREQUENCY,1.0e10 * STRAINFREQUENCY },            /* numberOfThCellsNaive  */
 {1.0e10, 1.0e10 * STRAINFREQUENCY,1.0e10 * STRAINFREQUENCY },            /* numberOfTcCellsNaive  */
  0.0,                        /* numberOfMacrophage  */
  0.0 ,                       /* numberOfDendritic  */
  0.0 ,                       /* epitheliaCell  */
  0.0 ,                       /* k2BloodInput_bCellNaive  */
  1.61e-2 * 175.0,            /* k2BloodInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodInput_thNaive  */
  0.0,                        /* k2BloodInput_tcNaive  */
  5.2,                 /* k2BloodInput_tcEffector  */
  0.0,                        /* k2BloodInput_Dendritic  */
  0.0,                        /* k2BloodInput_rbc  */
  0.0 ,                       /* k2BloodInput_platelets  */
  0.0 ,                       /* k2BloodInput_Macrophage  */
  0.0 ,                       /* k2BloodOutput_bCellNaive */
  0.0 ,                       /* k2BloodOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodOutput_thNaive  */
  0.0 ,                       /* k2BloodOutput_tcNaive  */
  0.0 ,                       /* k2LymphInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphInput_macrophageApc  */
  0.0 ,                       /* k2LymphInput_dendriticApc  */
  306.0 * 24.0 ,              /* k2LymphOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphOutput_tcEffector  */
  0.0 ,                       /* k2LymphOutput_macrophageApc  */
  0.0 ,                       /* k2LymphOutput_dendriticApc  */
  0.0 ,                       /* k2LymphOutput_thNaive  */
  0.0 ,                       /* k2LymphOutput_tcNaive  */
  0.0 ,                       /* k2macrophageReplicate  */
  0.0 ,                       /* k2dendriticReplicate  */
  5.2,                        /* k2BloodInput_plasmaCell  */
  0.0 ,                       /* k2LymphOutput_plasmaCell  */
  5.2,                         /* k2BloodInput_thEffector  */
  0.0 ,                       /* k2LymphOutput_thEffectorfector  */
  0.0 ,                       /* fdcGerminalCenters  */
   5.2,                        /* k2BloodInput_bCellMemory */   
   5.2,                        /* k2BloodInput_thMemory */      
   5.2,                        /* k2BloodInput_tcMemory */      
   0.0,                        /* k2BloodOutput_bCellMemory */  
   0.0,                        /* k2BloodOutput_thMemory */     
   0.0,                        /* k2BloodOutput_tcMemory */     
   4.0 * 24.0,                         /* k2LymphOutput_bCellMemory */  
   4.0 * 24.0,                         /* k2LymphOutput_thMemory */     
   4.0 * 24.0,                         /* k2LymphOutput_tcMemory */     
   0.0,                         /* k2LymphInput_bCellMemory */   
   0.0,                         /* k2LymphInput_thMemory */      
   0.0,                         /* k2LymphInput_tcMemory */      
   0.0,                        /* numberOfmastCell        */  
   2.0e11,                        /* numberOfeosinophil      */  
   0.0,                        /* k2BloodInput_mastCell   */  
   104.8,                        /* k2BloodInput_eosinophil */  
 },
{"respiratoryTract",
 {0.0,      0.0                   ,   0.0                   },            /* numberOfBCellsNaive  */
 {1.1e9 , 1.1e9 * STRAINFREQUENCY , 1.1e9 * STRAINFREQUENCY },            /* numberOfBCellsRecirculate  */
 {0.0   , 0.0                     , 0.0                     },            /* numberOfBCellsMarginalZone  */
 {9.7e9 , 9.7e9 * STRAINFREQUENCY , 9.7e9 * STRAINFREQUENCY },            /* numberOfThCellsNaive  */
 {2.0e10, 2.0e10 * STRAINFREQUENCY, 2.0e10 * STRAINFREQUENCY},            /* numberOfTcCellsNaive  */
  2.3e10,                      /* numberOfMacrophage  */
  2.3e8 ,                       /* numberOfDendritic  */
  1.6e11 ,                    /* epitheliaCell  */
  0.0 ,                       /* k2BloodInput_bCellNaive  */
  1.61e-2 * 168.0,            /* k2BloodInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodInput_thNaive  */
  0.0,                        /* k2BloodInput_tcNaive  */
  6.2,                 /* k2BloodInput_tcEffector  */
  0.0,                        /* k2BloodInput_Dendritic  */
  0.0,                        /* k2BloodInput_rbc  */
  0.0 ,                       /* k2BloodInput_platelets  */
  14.0 ,                      /* k2BloodInput_Macrophage  */
  0.0 ,                       /* k2BloodOutput_bCellNaive */
  0.0 ,                       /* k2BloodOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodOutput_thNaive  */
  0.0 ,                       /* k2BloodOutput_tcNaive  */
  0.0 ,                       /* k2LymphInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphInput_macrophageApc  */
  0.0 ,                       /* k2LymphInput_dendriticApc  */
  17.5 * 24.0 ,               /* k2LymphOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphOutput_tcEffector  */
  0.0 ,                       /* k2LymphOutput_macrophageApc  */
  0.0 ,                       /* k2LymphOutput_dendriticApc  */
  0.0 ,                       /* k2LymphOutput_thNaive  */
  0.0 ,                       /* k2LymphOutput_tcNaive  */
  4.0 * 24.0 ,              /* k2macrophageReplicate  */
  1.0  * 24.0 ,                       /* k2dendriticReplicate  */
  6.2,                        /* k2BloodInput_plasmaCell  */
  0.0 ,                       /* k2LymphOutput_plasmaCell  */
  6.2,                         /* k2BloodInput_thEffector  */
  0.0 ,                       /* k2LymphOutput_thEffectorfector  */
  0.0 ,                       /* fdcGerminalCenters  */
   6.2,                        /* k2BloodInput_bCellMemory */   
   6.2,                        /* k2BloodInput_thMemory */      
   6.2,                        /* k2BloodInput_tcMemory */      
   0.0,                        /* k2BloodOutput_bCellMemory */  
   0.0,                        /* k2BloodOutput_thMemory */     
   0.0,                        /* k2BloodOutput_tcMemory */     
   4.0 * 24.0,                          /* k2LymphOutput_bCellMemory */  
   4.0 * 24.0,                         /* k2LymphOutput_thMemory */     
   4.0 * 24.0,                         /* k2LymphOutput_tcMemory */     
   0.0,                         /* k2LymphInput_bCellMemory */   
   0.0,                         /* k2LymphInput_thMemory */      
   0.0,                         /* k2LymphInput_tcMemory */      
   4.0e8,                      /* numberOfmastCell        */  
   2.4e8,                      /* numberOfeosinophil      */  
   267.0,                        /* k2BloodInput_mastCell   */  
   0.13,                        /* k2BloodInput_eosinophil */  
 },                      
{"bronchialTest",
 { 0.0,              0.0                              ,0.0                              },   /* numberOfBCellsNaive  */
 { 1.1e9 * BRONCHIALFRACTION ,  1.1e9 * BRONCHIALFRACTION * STRAINFREQUENCY ,1.1e9 * BRONCHIALFRACTION * STRAINFREQUENCY },   /* numberOfBCellsRecirculate  */
 { 0.0            ,  0.0                              ,0.0                              },   /* numberOfBCellsMarginalZone  */
 { 9.7e9 * BRONCHIALFRACTION ,  9.7e9 * BRONCHIALFRACTION * STRAINFREQUENCY ,9.7e9 * BRONCHIALFRACTION * STRAINFREQUENCY },   /* numberOfThCellsNaive  */
 { 2.0e10 * BRONCHIALFRACTION,  2.0e10 * BRONCHIALFRACTION * STRAINFREQUENCY,2.0e10 * BRONCHIALFRACTION * STRAINFREQUENCY},   /* numberOfTcCellsNaive  */
   2.3e10 * BRONCHIALFRACTION,            /* numberOfMacrophage  */
  2.3e8 * BRONCHIALFRACTION,             /* numberOfDendritic  */
  1.6e11 * BRONCHIALFRACTION  ,          /* epitheliaCell  */
  0.0 ,                       /* k2BloodInput_bCellNaive  */
  1.61e-2 * 168.0 * BRONCHIALFRACTION,   /* k2BloodInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodInput_thNaive  */
  0.0,                        /* k2BloodInput_tcNaive  */
  BRONCHIALFLOWVALUE,                       /* k2BloodInput_tcEffector  */
  0.14 * BRONCHIALFRACTION ,             /* k2BloodInput_Dendritic  */
  0.0,                        /* k2BloodInput_rbc  */
  0.0 ,                       /* k2BloodInput_platelets  */
  14.0 * BRONCHIALFRACTION ,             /* k2BloodInput_Macrophage  */
  0.0 ,                       /* k2BloodOutput_bCellNaive */
  0.0 ,                       /* k2BloodOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodOutput_thNaive  */
  0.0 ,                       /* k2BloodOutput_tcNaive  */
  0.0 ,                       /* k2LymphInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphInput_macrophageApc  */
  0.0 ,                       /* k2LymphInput_dendriticApc  */
  17.5 * 24.0 ,               /* k2LymphOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphOutput_tcEffector  */
  8.33 * BRONCHIALFRACTION ,                /*  k2LymphOutput_macrophageApc  */
  8.33 * BRONCHIALFRACTION ,                      /*  k2LymphOutput_dendriticApc  */
  0.0 ,                       /* k2LymphOutput_thNaive  */
  0.0 ,                       /* k2LymphOutput_tcNaive  */
  1.0 * 24.0 ,              /* k2macrophageReplicate  */
  1.0 * 24.0 ,                       /* k2dendriticReplicate  */
  BRONCHIALFLOWVALUE,                        /* k2BloodInput_plasmaCell  */
  0.0 ,                       /* k2LymphOutput_plasmaCell  */
  BRONCHIALFLOWVALUE,                         /* k2BloodInput_thEffector  */
  0.0 ,                       /* k2LymphOutput_thEffectorfector  */
  0.0 ,                       /* fdcGerminalCenters  */
   BRONCHIALFLOWVALUE,                       /* k2BloodInput_bCellMemory */   
   BRONCHIALFLOWVALUE,                       /* k2BloodInput_thMemory */      
   BRONCHIALFLOWVALUE,                       /* k2BloodInput_tcMemory */      
   0.0,                        /* k2BloodOutput_bCellMemory */  
   0.0,                        /* k2BloodOutput_thMemory */     
   0.0,                        /* k2BloodOutput_tcMemory */     
   4.0 * 24.0,                          /* k2LymphOutput_bCellMemory */  
   4.0 * 24.0,                         /* k2LymphOutput_thMemory */     
   4.0 * 24.0,                         /* k2LymphOutput_tcMemory */     
   0.0,                         /* k2LymphInput_bCellMemory */   
   0.0,                         /* k2LymphInput_thMemory */      
   0.0,                         /* k2LymphInput_tcMemory */      
   4.0e8 * BRONCHIALFRACTION,                        /* numberOfmastCell        */  
   2.4e8 * BRONCHIALFRACTION,                        /* numberOfeosinophil      */  
   267.0 * BRONCHIALFRACTION,                      /* k2BloodInput_mastCell   */  
   0.13 * BRONCHIALFRACTION,                       /* k2BloodInput_eosinophil */  
 },
{"intestines",
 {0.0,      0.0                   ,  0.0                    },            /* numberOfBCellsNaive  */
 {7.6e9, 7.6e9 * STRAINFREQUENCY,7.6e9 * STRAINFREQUENCY },            /* numberOfBCellsRecirculate  */
 {0.0   , 0.0                     ,0.0                      },            /* numberOfBCellsMarginalZone  */
 {1.45e10, 1.45e10 * STRAINFREQUENCY,1.45e10 * STRAINFREQUENCY },            /* numberOfThCellsNaive  */
 {1.35e10, 1.35e10 * STRAINFREQUENCY,1.35e10 * STRAINFREQUENCY },            /* numberOfTcCellsNaive  */
  2.8e10,                      /* numberOfMacrophage  */
  2.8e9 ,                       /* numberOfDendritic  */
  2.7e11 ,                    /* epitheliaCell  */
  0.0 ,                       /* k2BloodInput_bCellNaive  */
  1.61e-2 * 273.0,            /* k2BloodInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodInput_thNaive  */
  0.0,                        /* k2BloodInput_tcNaive  */
  6.9,                 /* k2BloodInput_tcEffector  */
  0.0,                        /* k2BloodInput_Dendritic  */
  0.0,                        /* k2BloodInput_rbc  */
  0.0 ,                       /* k2BloodInput_platelets  */
  7.0 ,                       /* k2BloodInput_Macrophage  */
  0.0 ,                       /* k2BloodOutput_bCellNaive */
  0.0 ,                       /* k2BloodOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodOutput_thNaive  */
  0.0 ,                       /* k2BloodOutput_tcNaive  */
  0.0 ,                       /* k2LymphInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphInput_macrophageApc  */
  0.0 ,                       /* k2LymphInput_dendriticApc  */
  133.0 * 24.0 ,              /* k2LymphOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphOutput_tcEffector  */
  0.0 ,                       /* k2LymphOutput_macrophageApc  */
  0.0 ,                       /* k2LymphOutput_dendriticApc  */
  0.0 ,                       /* k2LymphOutput_thNaive  */
  0.0 ,                       /* k2LymphOutput_tcNaive  */
  4.0 * 24.0 ,              /* k2macrophageReplicate  */
  4.3 * 24.0 ,                       /* k2dendriticReplicate  */
  6.9,                        /* k2BloodInput_plasmaCell  */
  0.0 ,                       /* k2LymphOutput_plasmaCell  */
  6.9,                         /* k2BloodInput_thEffector  */
  0.0 ,                       /* k2LymphOutput_thEffectorfector  */
  0.0 ,                       /* fdcGerminalCenters  */
   6.9,                        /* k2BloodInput_bCellMemory */   
   6.9,                        /* k2BloodInput_thMemory */      
   6.9,                        /* k2BloodInput_tcMemory */      
   0.0,                        /* k2BloodOutput_bCellMemory */  
   0.0,                        /* k2BloodOutput_thMemory */     
   0.0,                        /* k2BloodOutput_tcMemory */     
   4.0 * 24.0,                         /* k2LymphOutput_bCellMemory */  
   4.0 * 24.0,                         /* k2LymphOutput_thMemory */     
   4.0 * 24.0,                         /* k2LymphOutput_tcMemory */     
   0.0,                         /* k2LymphInput_bCellMemory */   
   0.0,                         /* k2LymphInput_thMemory */      
   0.0,                         /* k2LymphInput_tcMemory */      
   3.5e9,                        /* numberOfmastCell        */  
   3.4e9,                        /* numberOfeosinophil      */  
   0.0,                        /* k2BloodInput_mastCell   */  
   0.0,                        /* k2BloodInput_eosinophil */  
 },
{"laminaProperiaTest",
 {0.0,      0.0                   ,  0.0                    },            /* numberOfBCellsNaive  */
 {7.6e9, 7.6e9 * LPFRACTION * STRAINFREQUENCY,7.6e9 * LPFRACTION * STRAINFREQUENCY },            /* numberOfBCellsRecirculate  */
 {0.0   , 0.0                     ,0.0                      },            /* numberOfBCellsMarginalZone  */
 {1.45e10, 1.45e10 * LPFRACTION * STRAINFREQUENCY,1.45e10 * LPFRACTION * STRAINFREQUENCY },            /* numberOfThCellsNaive  */
 {1.35e10, 1.35e10 * LPFRACTION * STRAINFREQUENCY,1.35e10 * LPFRACTION * STRAINFREQUENCY },            /* numberOfTcCellsNaive  */
  2.8e10 * LPFRACTION,                      /* numberOfMacrophage  */
  2.8e9  * LPFRACTION,                       /* numberOfDendritic  */
  2.7e11 * LPFRACTION ,                    /* epitheliaCell  */
  0.0 ,                       /* k2BloodInput_bCellNaive  */
  1.61e-2 * 273.0 * LPFRACTION,            /* k2BloodInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodInput_thNaive  */
  0.0,                        /* k2BloodInput_tcNaive  */
  LPFLOWVALUE,                 /* k2BloodInput_tcEffector  */
  0.7 * LPFRACTION,                        /* k2BloodInput_Dendritic  */
  0.0,                        /* k2BloodInput_rbc  */
  0.0 ,                       /* k2BloodInput_platelets  */
  7.0 * LPFRACTION ,                       /* k2BloodInput_Macrophage  */
  0.0 ,                       /* k2BloodOutput_bCellNaive */
  0.0 ,                       /* k2BloodOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodOutput_thNaive  */
  0.0 ,                       /* k2BloodOutput_tcNaive  */
  0.0 ,                       /* k2LymphInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphInput_macrophageApc  */
  0.0 ,                       /* k2LymphInput_dendriticApc  */
  133.0 * 24.0 ,              /* k2LymphOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphOutput_tcEffector  */
  13.6 * LPFRACTION / 2.0 ,                       /* k2LymphOutput_macrophageApc  */
  13.6 * LPFRACTION ,                       /* k2LymphOutput_dendriticApc  */
  0.0 ,                       /* k2LymphOutput_thNaive  */
  0.0 ,                       /* k2LymphOutput_tcNaive  */
  4.0 * 24.0 ,              /* k2macrophageReplicate  */
  4.3 * 24.0 ,                       /* k2dendriticReplicate  */
  LPFLOWVALUE,                        /* k2BloodInput_plasmaCell  */
  0.0 ,                       /* k2LymphOutput_plasmaCell  */
  LPFLOWVALUE,                         /* k2BloodInput_thEffector  */
  0.0 ,                       /* k2LymphOutput_thEffectorfector  */
  0.0 ,                       /* fdcGerminalCenters  */
   LPFLOWVALUE,                        /* k2BloodInput_bCellMemory */   
   LPFLOWVALUE,                        /* k2BloodInput_thMemory */      
   LPFLOWVALUE,                        /* k2BloodInput_tcMemory */      
   0.0,                        /* k2BloodOutput_bCellMemory */  
   0.0,                        /* k2BloodOutput_thMemory */     
   0.0,                        /* k2BloodOutput_tcMemory */     
   4.0 * 24.0,                         /* k2LymphOutput_bCellMemory */  
   4.0 * 24.0,                         /* k2LymphOutput_thMemory */     
   4.0 * 24.0,                         /* k2LymphOutput_tcMemory */     
   0.0,                         /* k2LymphInput_bCellMemory */   
   0.0,                         /* k2LymphInput_thMemory */      
   0.0,                         /* k2LymphInput_tcMemory */      
   3.5e9 * LPFRACTION,                        /* numberOfmastCell        */  
   3.4e9 * LPFRACTION,                        /* numberOfeosinophil      */  
   0.0,                        /* k2BloodInput_mastCell   */  
   0.0,                        /* k2BloodInput_eosinophil */  
 },
{"boneMarrow",
 {0.0 , 0.0 , 0.0 },                /* numberOfBCellsNaive  */
 {0.0 , 0.0 , 0.0 },                /* numberOfBCellsRecirculate  */
 {0.0 , 0.0 , 0.0 },                /* numberOfBCellsMarginalZone  */
 {0.0 , 0.0 , 0.0 },                /* numberOfThCellsNaive  */
 {0.0 , 0.0 , 0.0 },                /* numberOfTcCellsNaive  */
  0.0 ,                       /* numberOfMacrophage  */
  0.0 ,                       /* numberOfDendritic  */
  0.0 ,                       /* epitheliaCell  */
  0.0 ,                       /* k2BloodInput_bCellNaive  */
  0.0 ,                       /* k2BloodInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodInput_thNaive  */
  0.0,                        /* k2BloodInput_tcNaive  */
  6.9,                 /* k2BloodInput_tcEffector  */
  0.0,                        /* k2BloodInput_Dendritic  */
  0.0,                        /* k2BloodInput_rbc  */
  0.0 ,                       /* k2BloodInput_platelets  */
  0.0 ,                       /* k2BloodInput_Macrophage  */
  0.0 ,                       /* k2BloodOutput_bCellNaive */
  0.0 ,                       /* k2BloodOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodOutput_thNaive  */
  0.0 ,                       /* k2BloodOutput_tcNaive  */
  0.0 ,                       /* k2LymphInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphOutput_tcEffector  */
  0.0 ,                       /* k2LymphOutput_macrophageApc  */
  0.0 ,                       /* k2LymphOutput_dendriticApc  */
  0.0 ,                       /* k2LymphOutput_thNaive  */
  0.0 ,                       /* k2LymphOutput_tcNaive  */
  0.0 ,                       /* k2macrophageReplicate  */
  0.0 ,                       /* k2dendriticReplicate  */
  6.9,                        /* k2BloodInput_plasmaCell  */
  0.0 ,                       /* k2LymphOutput_plasmaCell  */
  6.9,                         /* k2BloodInput_thEffector  */
  0.0 ,                       /* k2LymphOutput_thEffectorfector  */
  0.0 ,                       /* fdcGerminalCenters  */
   0.0,                        /* k2BloodInput_bCellMemory */   
   0.0,                        /* k2BloodInput_thMemory */      
   0.0,                        /* k2BloodInput_tcMemory */      
   0.0,                        /* k2BloodOutput_bCellMemory */  
   0.0,                        /* k2BloodOutput_thMemory */     
   0.0,                        /* k2BloodOutput_tcMemory */     
   0.0,                                /* k2LymphOutput_bCellMemory */  
   0.0,                                /* k2LymphOutput_thMemory */     
   0.0,                                /* k2LymphOutput_tcMemory */     
   0.0,                         /* k2LymphInput_bCellMemory */   
   0.0,                         /* k2LymphInput_thMemory */      
   0.0,                         /* k2LymphInput_tcMemory */      
   0.0,                        /* numberOfmastCell        */  
   0.0,                        /* numberOfeosinophil      */  
   0.0,                        /* k2BloodInput_mastCell   */  
   0.0,                        /* k2BloodInput_eosinophil */  
 },
{"lymphJunction",
 {0.0 , 0.0 , 0.0 },                /* numberOfBCellsNaive  */
 {0.0 , 0.0 , 0.0 },                /* numberOfBCellsRecirculate  */
 {0.0 , 0.0 , 0.0 },                /* numberOfBCellsMarginalZone  */
 {0.0 , 0.0 , 0.0 },                /* numberOfThCellsNaive  */
 {0.0 , 0.0 , 0.0 },                /* numberOfTcCellsNaive  */
  0.0 ,                       /* numberOfMacrophage  */
  0.0 ,                       /* numberOfDendritic  */
  0.0 ,                       /* epitheliaCell  */
  0.0 ,                       /* k2BloodInput_bCellNaive  */
  0.0 ,                       /* k2BloodInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodInput_thNaive  */
  0.0,                        /* k2BloodInput_tcNaive  */
  0.0,                 /* k2BloodInput_tcEffector  */
  0.0,                        /* k2BloodInput_Dendritic  */
  0.0,                        /* k2BloodInput_rbc  */
  0.0 ,                       /* k2BloodInput_platelets  */
  0.0 ,                       /* k2BloodInput_Macrophage  */
  0.0 ,                       /* k2BloodOutput_bCellNaive */
  0.0 ,                       /* k2BloodOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2BloodOutput_thNaive  */
  0.0 ,                       /* k2BloodOutput_tcNaive  */
  0.0 ,                       /* k2LymphInput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphInput_macrophageApc  */
  0.0 ,                       /* k2LymphInput_dendriticApc  */
  0.0 ,                       /* k2LymphOutput_bCellNaiveRecirculate  */
  0.0 ,                       /* k2LymphOutput_tcEffector  */
  0.0 ,                       /* k2LymphOutput_macrophageApc  */
  0.0 ,                       /* k2LymphOutput_dendriticApc  */
  0.0 ,                       /* k2LymphOutput_thNaive  */
  0.0 ,                       /* k2LymphOutput_tcNaive  */
  0.0 ,                       /* k2macrophageReplicate  */
  0.0 ,                       /* k2dendriticReplicate  */
  0.0,                        /* k2BloodInput_plasmaCell  */
  0.0 ,                       /* k2LymphOutput_plasmaCell  */
  0.0,                         /* k2BloodInput_thEffector  */
  0.0 ,                       /* k2LymphOutput_thEffectorfector  */
  0.0 ,                       /* fdcGerminalCenters  */
   0.0,                        /* k2BloodInput_bCellMemory */   
   0.0,                        /* k2BloodInput_thMemory */      
   0.0,                        /* k2BloodInput_tcMemory */      
   0.0,                        /* k2BloodOutput_bCellMemory */  
   0.0,                        /* k2BloodOutput_thMemory */     
   0.0,                        /* k2BloodOutput_tcMemory */     
   0.0,                                /* k2LymphOutput_bCellMemory */  
   0.0,                                /* k2LymphOutput_thMemory */     
   0.0,                                /* k2LymphOutput_tcMemory */     
   0.0,                         /* k2LymphInput_bCellMemory */   
   0.0,                         /* k2LymphInput_thMemory */      
   0.0,                    /* k2LymphInput_tcMemory */      
   0.0,                        /* numberOfmastCell        */  
   0.0,                        /* numberOfeosinophil      */  
   0.0,                        /* k2BloodInput_mastCell   */  
   0.01234,                        /* check point k2BloodInput_eosinophil */  
 },
};
   

immuneCellEntry  immuneCellData[] = {
//                                                                                                                      (P=plasma,T=total)
//                                  initial           initial                  quantity  concentration  volume    quantity    which    profile
//       name                    Concentration        profile                     units     units       conFact    conFact    volume   style   
{'R', "igG"                    ,{ 600.0 , 0.0} ,{{0.0,1.0,0.0},{0.0,1.0,0.0}}  , "mg"       , "mg/dl" , 1.0e5         , 146.0 , 'P' ,  '0'}      ,
{'R', "igM"                    ,{  40.0 , 0.0} ,{{1.0,0.0,0.0},{1.0,0.0,0.0}}  , "mg"       , "mg/dl" , 1.0e5         , 970.0 , 'P' ,  '0'}      ,
{'R', "igA"                    ,{  60.0 , 0.0} ,{{0.0,0.0,1.0},{0.0,0.0,1.0}}  , "mg"       , "mg/dl" , 1.0e5         , 160.0 , 'P' ,  '0'}      ,
{'R', "bCellNaive"             ,{ 403.0 , 403.0 * STRAINFREQUENCY} ,{{1.0,0.0,0.0},{1.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T', 'b'}      ,
{'R', "bCellNaiveRecirculate"  ,{ 186.0 , 186.0 * STRAINFREQUENCY} ,{{1.0,0.0,0.0},{1.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,'b'}      ,
{'R', "plasmaCell"             ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' , 'b' }      ,
{'R', "thNaive"                ,{1278.0 , 1278.0 * STRAINFREQUENCY} ,{{1.0,0.0,0.0},{1.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,'t'}      ,
{'R', "tcNaive"                ,{ 620.0 , 620.0 * STRAINFREQUENCY} ,{{1.0,0.0,0.0},{1.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' , 't'}      ,
{'R', "thEffector"             ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,  't'}      ,
{'R', "tcEffector"             ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,            't' }      ,
{'R', "bCellMemory"            ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,            't' }      ,
{'R', "thMemory"               ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,            't' }      ,
{'R', "tcMemory"               ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,            't' }      ,
                                                                 
{'l', "igG"                    ,{   0.0 , 0.0} ,{{0.0,1.0,0.0},{0.0,1.0,0.0}}  , "mg"       , "mg/dl" , 1.0e5         , 146.0 , 'P' ,  '0'}      ,
{'l', "igM"                    ,{   0.0 , 0.0} ,{{1.0,0.0,0.0},{1.0,0.0,0.0}}  , "mg"       , "mg/dl" , 1.0e5         , 970.0 , 'P' ,  '0'}      ,
{'l', "igA"                    ,{   0.0 , 0.0} ,{{0.0,0.0,1.0},{0.0,0.0,1.0}}  , "mg"       , "mg/dl" , 1.0e5         , 160.0 , 'P' ,  '0'}      ,
{'l', "bCellNaiveRecirculate"  ,{1000.0 , 1000.0 * STRAINFREQUENCY} ,{{1.0,0.0,0.0},{1.0,0.0,0.0}}        , "#"       , "#/ul" , 1.0         , 1.0 , 'T' ,      'b'}      ,
{'l', "plasmaCell"             ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' , 'b' }      ,
{'l', "thNaive"                ,{6600.0 , 6600.0 * STRAINFREQUENCY} ,{{1.0,0.0,0.0},{1.0,0.0,0.0}}        , "#"       , "#/ul" , 1.0         , 1.0 , 'T' ,      't'}      ,
{'l', "tcNaive"                ,{2000.0 , 2000.0 * STRAINFREQUENCY} ,{{1.0,0.0,0.0},{1.0,0.0,0.0}}        , "#"       , "#/ul" , 1.0         , 1.0 , 'T' ,      't'}      ,
{'l', "thEffector"             ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,  't'}      ,
{'l', "tcEffector"             ,{ 0.0   , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}      , "#"       , "#/ul" , 1.0         , 1.0        , 'T' , 't' }      ,
{'l', "macrophageApc"          ,{ 0.0   , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}      , "#"       , "#/ul" , 1.0         , 1.0 , 'T' ,        't'}      ,
{'l', "dendriticApc"           ,{ 0.0   , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}      , "#"       , "#/ul" , 1.0         , 1.0 , 'T' ,        't'}      ,
{'l', "bCellMemory"            ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,            't' }      ,
{'l', "thMemory"               ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,            't' }      ,
{'l', "tcMemory"               ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,            't' }      ,
                                                                 
{'a', "igG"                    ,{   0.0 , 0.0} ,{{0.0,1.0,0.0},{0.0,1.0,0.0}}  , "mg"       , "mg/dl" , 1.0e5         , 146.0 , 'P' ,  '0'}      ,
{'a', "igM"                    ,{   0.0 , 0.0} ,{{1.0,0.0,0.0},{1.0,0.0,0.0}}  , "mg"       , "mg/dl" , 1.0e5         , 970.0 , 'P' ,  '0'}      ,
{'a', "igA"                    ,{   0.0 , 0.0} ,{{0.0,0.0,1.0},{0.0,0.0,1.0}}  , "mg"       , "mg/dl" , 1.0e5         , 160.0 , 'P' ,  '0'}      ,
{'a', "bCellNaiveRecirculate"  ,{60.0   , 60.0 * STRAINFREQUENCY} ,{{1.0,0.0,0.0},{1.0,0.0,0.0}}      , "#"       , "#/ul" , 1.0         , 1.0 , 'T' ,        'b'}      ,
{'a', "plasmaCell"             ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' , 'b' }      ,
{'a', "thNaive"                ,{ 0.0   , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}      , "#"       , "#/ul" , 1.0         , 1.0 , 'T' ,        't'}      ,
{'a', "tcNaive"                ,{ 0.0   , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}      , "#"       , "#/ul" , 1.0         , 1.0 , 'T' ,        't'}      ,
{'a', "thEffector"             ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,  't'}      ,
{'a', "tcEffector"             ,{ 0.0   , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}      , "#"       , "#/ul" , 1.0         , 1.0        , 'T' , 't' }      ,
{'a', "macrophageApc"          ,{ 0.0   , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}      , "#"       , "#/ul" , 1.0         , 1.0 , 'T' ,        't'}      ,
{'a', "dendriticApc"           ,{ 0.0   , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}      , "#"       , "#/ul" , 1.0         , 1.0 , 'T' ,        't'}      ,
{'a', "bCellMemory"            ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,            't' }      ,
{'a', "thMemory"               ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,            't' }      ,
{'a', "tcMemory"               ,{   0.0 , 0.0} ,{{0.0,0.0,0.0},{0.0,0.0,0.0}}  , "#"       , "#/ul" , 1.0         , 1.0        , 'T' ,            't' }      ,
};

substanceEntry  substanceData[] = {
//                                                                                       (P=plasma,T=total)
//                                  initial    quantity  concentration  volume   quantity  which       
//       name                    Concentration  units     units          conFact  conFact  volume   auxiliary                                    
// kidney
{'c',  "angiotensin2"             ,    1.0     , "xg"      , "xg/L", 1.0e6        , 1.0 , 'P' ,0 }      ,
// hypothalamus
{'c',  "trh"                      ,   60.0     , "pg"      , "pg/ml", 1.0e3       , 3.62e6 , 'P' ,0 }     ,
{'c',  "crh"                      ,    0.1     , "ng"      , "ng/ml", 1.0e3        , 4.5e6 , 'P' ,0 }      ,
{'c',  "ghrh"                     ,    1.0     , "xg"      , "xg/L", 1.0e6        , 1.0 , 'P' ,0 }      ,
{'c',  "somatostatin"             ,    2.0     , "ng"      , "ng/dl", 1.0e5       , 1.64e3 , 'P' ,0 }     ,
{'c',  "dopamine"                 ,    1.0     , "xg"      , "xg/L", 1.0e6        , 1.0 , 'P' ,0 }      ,
// pituitary
{'c',  "prl"                      ,   10.0     , "ng"      , "ng/ml", 1.0e3       , 1.0 , 'P' ,0 }     ,
{'c',  "acth"                     ,   50.0     , "pg"      , "pg/ml", 1.0e3       , 4.5e9 , 'P' ,0 }     ,
{'c',  "vasopressin"              ,    1.0     , "pg"      , "pg/ml", 1.0e3       , 1.0 , 'P' ,0 }     ,
{'c',  "growthHormone"            ,    3.0     , "ng"      , "ng/ml", 1.0e3       , 1.0 , 'P' ,0 }     ,
{'c',  "tsh"                      ,    1.0     , "uU"      , "uU/ml", 1.0e3       , 1.0 , 'P' ,0 }     ,
// thyroid
{'c',  "t4"                       ,    8.0     , "ug"      , "ug/dl", 1.0e5       , 777.0 , 'P' ,0 }     ,
{'c',  "t3"                       ,    0.1     , "ug"      , "ug/dl", 1.0e5       , 650.0 , 'P' ,0 }     ,
// adrenal
{'c',  "cortisol"                 ,   10.0     , "ug"      , "ug/dl", 1.0e5       , 362.0 , 'P' ,0 }     ,
{'c',  "aldosterone"              ,    6.0     , "ng"      , "ng/dl", 1.0e5       , 1.0 , 'P' ,0 }     ,
{'c',  "epinephrine"              ,   34.0     , "pg"      , "pg/ml", 1.0e3       , 183.0e6 , 'P' ,0 }     ,
{'c',  "norepinephrine"           ,  228.0     , "pg"      , "pg/ml", 1.0e3       , 1.0 , 'P' ,0 }     ,
// liver
{'c',  "igf1"                     ,  300.0     , "ug"      , "ug/L", 1.0e6        , 1.0 , 'P' ,0 }      ,
// pancreas
 {'c',  "insulin"                  ,   11.6     , "uU"      , "uU/ml", 1.0e3       , 1.449e8 , 'P' ,0 }     ,
 {'c',  "glucagon"                 ,   72.0     , "pg"      , "pg/ml", 1.0e3       , 3.485e9 , 'P' ,0 }     ,
// small intestine, stomach
{'c',  "gastrin"                  ,   50.0     , "pg"      , "pg/ml", 1.0e3       , 2.1e9 , 'P' ,0 }     ,
{'c',  "cck"                      ,    3.9     , "ng"      , "ng/ml", 1.0e3       , 3.9e9 , 'P' ,0 }     ,
{'c',  "secretin"                 ,    8.0     , "pg"      , "pg/ml", 1.0e3       , 3.0e9 , 'P' ,0 }     ,
{'c',  "gip"                      ,  250.0     , "pg"      , "pg/ml", 1.0e3       , 5.0e9 , 'P' ,0 }     ,
// nutrients, etc.
{'c',  "oxygen"                   ,  8900.0    , "uMol"    , "uMol/L", 1.0e6       , 1.0 , 'T' ,0 }      ,
{'c',  "CO2"                   ,  48000.0   , "uMol"    , "uMol/L", 1.0e6       , 1.0 , 'T' ,0 }      ,
{'c',  "Na"                       ,  144.0     , "mEq"     , "mEq/L", 1.0e6       , 1.0e-3 , 'P' ,0 }      ,
{'c',  "potassium"                ,    4.5     , "mEq"     , "mEq/L", 1.0e6       , 1.0e-3 , 'P' ,0 }      ,
{'c',  "iodine"                   ,    0.6     , "ug"      , "ug/dl", 1.0e5       , 127.0 , 'P' ,0 }     ,

{'c', "monocyte"               ,  47.0       , "#"       , "#/ul" , 1.0         , 1.0       , 'T' , 0             }      ,
{'c', "eosinophil"             ,  203.0       , "#"       , "#/ul" , 1.0         , 1.0       , 'T' , 0             }      ,
{'c', "mastCell"             ,  0.6       , "#"       , "#/ul" , 1.0         , 1.0       , 'T' , 0             }      ,
{'c', "platelets"               ,  250.0e3       , "#"       , "#/ul" , 1.0         , 1.0       , 'T' , 0             }      ,
{'c', "rbc"               ,  5.0e6       , "#"       , "#/ul" , 1.0         , 1.0       , 'T' , 0             }      ,
{'c',  "gmcsf"                  ,   0.0     , "ng"      , "ng/ml", 1.0e3       , 5.0e7 , 'P' ,0 }     ,
{'c',  "il3"                  ,   0.0     , "ng"      , "ng/ml", 1.0e3       , 1.8e7 , 'P' ,0 }     ,
{'c',  "il5"                  ,   0.0     , "ng"      , "ng/ml", 1.0e3       , 3.0e7 , 'P' ,0 }     ,

// {'c',  "glucose"                  ,  56.0     , "mg"      , "mg/dl", 1.0e5       , 0.18 , 'P' ,0 }     ,
{'c',  "glucose"                  ,   90.0     , "mg"      , "mg/dl", 1.0e5       , 0.18 , 'P' ,0 }     ,
{'c',  "aminoAcids"               ,   40.0     , "mg"      , "mg/dl", 1.0e5       , 0.115 , 'P' ,0 }     ,
{'c',  "ketones"                  ,   0.3     , "mg"      , "mg/dl", 1.0e5       , 0.1 , 'P' ,0 }     ,
{'c',  "lactate"                  ,     9.0   , "mg"      , "mg/dl", 1.0e5       , 9.0e-2 , 'P' ,0 }     ,
{'c',  "glycerol"                 ,   50.0    , "uMol"    , "uMol/L", 1.0e6       , 1.0 , 'P' ,0 }     ,
{'c',  "fattyAcids"               ,   5.7     , "mg"      , "mg/dl", 1.0e5       , .256 , 'P' ,0 }     ,

{'c',  "vldl"                     ,   15.0     , "mg"      , "mg/dl", 1.0e5       , 7.5e3 , 'P' ,0 }     ,
{'c',  "ldl"                      ,  120.0     , "mg"      , "mg/dl", 1.0e5       , 2.8e3 , 'P' ,0 }     ,
{'c',  "hdl"                      ,   50.0     , "mg"      , "mg/dl", 1.0e5       , 200.0 , 'P' ,0 }     ,
{'c',  "idl"                      ,    4.1     , "mg"      , "mg/dl", 1.0e5       , 3.7e3 , 'P' ,0 }     ,
{'c',  "chylomicrons"             ,    0.0     , "mg"      , "mg/dl", 1.0e5       , 400.0e3 , 'P' ,0 }     ,
{'c',  "chylomicronRemnant"       ,    0.0     , "mg"      , "mg/dl", 1.0e5       , 1.36e5 , 'P' ,0 }     ,

{'c',  "ammonia"                  ,     30.0   , "ug"      , "ug/dl", 1.0e5       , 1.0 , 'P' ,0 }     ,
// {'c',  "acetoaceticAcid"          ,     10.0   , "mg"      , "mg/dl", 1.0e5       , 1.0 , 'P' ,0 }  ,
{'c',  "urea"                     ,     34.0   , "mg"      , "mg/dl", 1.0e5       , 1.0 , 'P' ,0 }     ,
{'c',  "plasmaProteins"           ,      7.3   , "g"       , "g/dl", 1.0e5        , 4.4e-2 , 'P' ,0 }  ,
{'c',  "bilirubin"                ,      0.5   , "mg"      , "mg/dl", 1.0e5       , 1.0 , 'P' ,0 }     ,
{'c',  "bileSalts"                ,      0.05  , "mg"      , "mg/dl", 1.0e5       , 4.0e-4 , 'P' ,0 }    ,


{'d',  "proteinSolid"             ,     0.0    , "g"       , "g/dl", 1.0e5        , 1.15e-2 , 'T' ,0 }     ,
{'d',  "proteinChyme"             ,     0.0    , "g"       , "g/dl", 1.0e5        , 1.15e-2 , 'T' ,0 }     ,
{'d',  "carbohydrates"            ,     0.0    , "g"       , "g/dl", 1.0e5        , 1.8e-2 , 'T' ,0 }     ,
{'d',  "fats"                     ,     0.0    , "g"       , "g/dl", 1.0e5        , 1.0 , 'T' ,0 }     ,
{'d',  "peptides"                 ,     0.0    , "g"       , "g/dl", 1.0e5        , 1.15e-3, 'T' ,0 }     ,
{'d',  "aminoAcids"               ,     0.0    , "mg"      , "mg/dl", 1.0e5       , 0.115 , 'T' ,0 }     ,
{'d',  "triglycerides"            ,     0.0    , "g"       , "g/dl", 1.0e5        , 8.3e-4 , 'T' ,0 }     ,
{'d',  "aminopeptidase"           ,     0.0    , "kunits"  , "kunits/ml", 1.0e3   , 1.0 , 'T' ,0 }     ,
{'d',  "pepsin"                   ,     0.0   , "kunits"  , "kunits/ml", 1.0e3   , 1.0 , 'T' ,0 }      ,
{'d',  "bicarbonate"              ,     0.0    , "mEq"     , "mEq/L", 1.0e6       , 1.0e-3 , 'T' ,0 }      ,
{'d',  "bilirubin"                ,     0.0    , "g"       , "g/dl", 1.0e5        , 1.0 , 'T' ,0 }     ,
{'d',  "trypsin"                  ,     0.0    , "kunits"  , "kunits/ml", 1.0e3   , 1.0 , 'T' ,0 }     ,
{'d',  "chymotrypsin"             ,     0.0    , "kunits"  , "kunits/ml", 1.0e3   , 1.0 , 'T' ,0 }     ,
{'d',  "carboxypeptidase"         ,     0.0    , "kunits"  , "kunits/ml", 1.0e3   , 1.0 , 'T' ,0 }     ,
{'d',  "lipase"                   ,     0.0    , "kunits"  , "kunits/ml", 1.0e3   , 1.0 , 'T' ,0 }     ,
{'d',  "amylase"                  ,     0.0    , "kunits"  , "kunits/ml", 1.0e3   , 1.0 , 'T' ,0 }     ,
{'d',  "cholesterol"              ,     0.0    , "g"       , "g/dl", 1.0e5        , 1.0 , 'T' ,0 }     ,
{'d',  "fattyAcids"               ,     0.0    , "g"       , "g/dl", 1.0e5        , 1.0 , 'T' ,0 }     ,
{'d',  "bileSalts"                ,     0.0    , "g"       , "g/dl", 1.0e5        , 4.0e-4 , 'T' ,0 }  ,
{'d',  "hcl"                      ,     0.0    , "mEq"     , "mEq/L", 1.0e6       , 1.0e-3 , 'T' ,0 }     ,

{'b',  "bicarbonate"              ,    20.0    , "mEq"     , "mEq/L", 1.0e6       , 1.0e-3 , 'T' ,0 }      ,
{'b',  "bilirubin"                ,     0.0    , "g"       , "g/dl", 1.0e5        , 1.0 , 'T' ,0 }     ,
{'b',  "trypsin"                  ,     0.0       , "kunits"  , "kunits/ml", 1.0e3   , 1.0 , 'T' ,0 }     ,
{'b',  "chymotrypsin"             ,     0.0       , "kunits"  , "kunits/ml", 1.0e3   , 1.0 , 'T' ,0 }     ,
{'b',  "carboxypeptidase"         ,     0.0       , "kunits"  , "kunits/ml", 1.0e3   , 1.0 , 'T' ,0 }     ,
{'b',  "lipase"                   ,     0.0       , "kunits"  , "kunits/ml", 1.0e3   , 1.0 , 'T' ,0 }     ,
{'b',  "amylase"                  ,     0.0       , "kunits"  , "kunits/ml", 1.0e3   , 1.0 , 'T' ,0 }     ,
{'b',  "cholesterol"              ,     1.0 /* ? */   , "g"       , "g/dl", 1.0e5        , 3.85e-4 , 'T' ,0 }     ,
{'b',  "fattyAcids"               ,     0.0    , "g"       , "g/dl", 1.0e5        , 1.0 , 'T' ,0 }     ,
{'b',  "bileSalts"                ,     1.5       , "g"       , "g/dl", 1.0e5        , 4.0e-4 , 'T' ,0 }  ,

{'l',  "chylomicrons"             ,    0.0     , "mg"      , "mg/dl", 1.0e5       , 400e3 , 'P' ,0 }     ,

{'r',  "glucose"                  ,   90.0     , "mg"      , "mg/dl", 1.0e5       , 0.18 , 'P' ,0 }     ,
{'r',  "t4"                       ,    8.0     , "ug"      , "ug/dl", 1.0e5       , 777.0 , 'P' ,0 }     ,
{'r',  "t3"                       ,    0.1     , "ug"      , "ug/dl", 1.0e5       , 650.0 , 'P' ,0 }     ,
};


vesselEntry  vesselData[] = {
/*                                mm3/msec  mm3/msec   mm3        mm3 */
/*                               flowOut    flowIn  TotVolume   PlasmaVol      quantity      length   pressure  previous  next */

{'c', "pulmonaryCapillary",      82.5,       -1.0,   864000.0,  475200.0,   7161241700.0,      0.31,      6.97, "venaCava",            "aorta"},
{'c', "venaCava",                82.5,       -1.0,  3432792.0, 1888036.0,            1.0,    550.00,      1.02, "genericCapillary",    "pulmonaryCapillary"},
{'c', "aorta",                   28.3,       -1.0,   702000.0,  386100.0,            1.0,    550.00,     99.53, "pulmonaryCapillary",  "genericCapillary"},
{'c', "cerebralCapillary",       12.49,      12.5,    55621.0,   30592.0,   2785211504.0,      1.00,     12.02, "aorta",               "venaCava"},
{'c', "hypophysealPortalVein",    0.01,       0.01,     118.0,      65.0,           11.0,     20.00,     21.73, "cerebralCapillary",   "venaCava"},
{'c', "hepaticSinusoid",         21.7,        4.2,   105458.0,   58002.0,    596831037.0,      2.07,      1.86, "aorta",  "venaCava"},
{'c', "portalVein",              17.5,       15.0,    23090.0,   12700.0,            1.0,    150.00,      8.95, "aorta",  "hepaticSinusoid"},
{'c', "splenicCapillary",        2.5,         2.5,     6075.0,    3341.0,    596831037.0,      0.81,     15.81, "aorta",  "portalVein"},
{'c', "glomularCapillary",       20.0,       20.0,    88994.0,   40047.0,    273547558.0,      1.00,     59.55, "aorta",  "venaCava"},
{'c', "genericCapillary",        28.3,       -1.0,   119852.0,   65919.0,            1.0,     114.0,     15.51, "aorta",  "venaCava"},

{'R', "bloodReservoir",          -1.0,       -1.0,  5400000.0,  2970000.0,           1.0,       1.0,     15.51, "_end",  "_end"},

{'d', "sigmoidColon",              0.10,       -1.0,      3.8e6,    3.8e6,      1.0,    300.00,      0.01,"descendingColon","_end"},
{'d', "descendingColon",           0.1,        -1.0,     3.8e6,    3.8e6,      1.0,    300.00,      0.01,"transverseColon","sigmoidColon"},
{'d', "transverseColon",           0.1,        -1.0,     3.8e6,    3.8e6,      1.0,    300.00,      0.01,"ascendingColon","descendingColon"},
{'d', "ascendingColon",            0.1,        -1.0,     3.8e6,    3.8e6,      1.0,    300.00,      0.01,"ileum","transverseColon"},
{'d', "ileum",                     0.2,        -1.0,     4.2e6,    4.2e6,      1.0,    920.00,      0.01,"jejunum","ascendingColon"},
{'d', "jejunum",                   0.2,        -1.0,     4.2e6,    4.2e6,      1.0,    920.00,      0.01,"duodenum","ileum"},
{'d', "duodenum",                  0.2,        -1.0,     4.2e6,    4.2e6,      1.0,    920.00,      0.01,"stomach","jejunum"},
{'d', "stomach",                  15.4,        -1.0,     1.0e6,    1.0e6,      1.0,    100.00,      0.01,"esophagus","duodenum"},
{'d', "esophagus",               1500.0,       -1.0,     1.0e6,    1.0e6,      1.0,    230.00,      0.01,"_end","stomach"},

{'b', "commonBileDuct",           58.3 ,       -1.0,     10.0e4,   10.0e4,      1.0,    100.00,      0.01,"commonHepaticDuct","_end"},
{'b', "commonHepaticDuct",        58.3 ,       -1.0,      5.0e4,    5.0e4,      1.0,    100.00,      0.01,"_end","commonBileDuct"},
{'b', "pancreaticDuct",           58.3 ,       -1.0,      5.0e4,    5.0e4,      1.0,    100.00,      0.01,"_end","commonBileDuct"},

{'l', "thoracicDuct5",            0.0347,       -1.0,    2.0e5,    2.0e5,      1.0,    100.00,      0.01, "thoracicDuct4","_end"},
{'l', "thoracicDuct4",            4.167e4,      -1.0,    1.0e5,    1.0e5,      1.0,    100.00,      0.01, "thoracicDuct3","thoracicDuct5"},
{'l', "thoracicDuct3",            4.167e4,      -1.0,    1.0e5,    1.0e5,      1.0,    100.00,      0.01, "thoracicDuct2","thoracicDuct4"},
{'l', "thoracicDuct2",            4.167e4,      -1.0,    1.0e5,    1.0e5,      1.0,    100.00,      0.01, "thoracicDuct1","thoracicDuct3"},
{'l', "thoracicDuct1",            4.167e4,      -1.0,    1.0e5,    1.0e5,      1.0,    100.00,      0.01, "lymphaticVein","thoracicDuct2"},

{'a', "hepaticAfferent",              -1.0,     -1.0,    33000,    33000,      1.0,    100.00,      0.01, "_end","_end"},
{'a', "subcutaneousAfferent",         -1.0,     -1.0,   440000,   440000,      1.0,    100.00,      0.01, "_end","_end"},
{'a', "miscellaneousAfferent",        -1.0,     -1.0,   160000,   160000,      1.0,    100.00,      0.01, "_end","_end"},
{'a', "mediastinalAfferent",          -1.0,     -1.0,   200000,   200000,      1.0,    100.00,      0.01, "_end","_end"},
{'a', "mediastinalAfferentTest",      -1.0,     -1.0,     1500,     1500,      1.0,    100.00,      0.01, "_end","_end"},
{'a', "mesentericAfferent",           -1.0,     -1.0,   260000,   260000,      1.0,    100.00,      0.01, "_end","_end"},
{'a', "mesentericAfferentTest",       -1.0,     -1.0,     2600,     2600,      1.0,    100.00,      0.01, "_end","_end"},

{'r', "interstitialReservoir",        -1.0,     -1.0,    11.5e6,  11.5e6,      1.0,    100.00,      0.01, "_end","_end"},
};

/* end physiological data */

#define  NUMBEROFTISSUECONSTANTS    (sizeof(tissueConstants) / sizeof(tissueConstant))
#define  TOTALSUBSTANCES    (sizeof(substanceData) / sizeof(substanceEntry))
#define  TOTALIMMUNECELLS    (sizeof(immuneCellData) / sizeof(immuneCellEntry))
#define  NUMBEROFVESSELS    (sizeof(vesselData) / sizeof(vesselEntry))
#define  INDEX_END    (-1)

Nerve  smallIntestineNerve;


int  VesselSegment::vesselIndex = 0 ;


void  VesselSegment::HelpPrint ()
{
    int  i;
    char  ch;

    for (i = 0; i < TOTALSUBSTANCES; i++) {
        ch = substanceData[i].type ;
        switch (ch) {
        case  'c':
            printf("    static  int  blood_%s  = printCapillary->FindSubstanceIndex(\"%s\") ;\n",substanceData[i].name,substanceData[i].name);
            break;
        case  'R':
            printf("    static  int  reservoir_%s  = printReservoir->FindSubstanceIndex(\"%s\") ;\n",substanceData[i].name,substanceData[i].name);
            break;
        case  'l':
            printf("    static  int  lymph_%s  = printEfferent->FindSubstanceIndex(\"%s\") ;\n",substanceData[i].name,substanceData[i].name);
            break;
        case  'a':
            printf("    static  int  afferent_%s  = printAfferent->FindSubstanceIndex(\"%s\") ;\n",substanceData[i].name,substanceData[i].name);
            break;
        default:
            break;
        } /* switch */
    } /* forLoop */

    for (i = 0; i < TOTALSUBSTANCES; i++) {
        ch = substanceData[i].type ;
        switch (ch) {
        case  'c':
            printf("    printCapillary->PrintSubstance(blood_%s, 'c');\n",substanceData[i].name);
            break;
        case  'R':
            printf("    printReservoir->PrintSubstance(reservoir_%s, 'c');\n",substanceData[i].name);
            break;
        case  'l':
            printf("    printEfferent->PrintSubstance(lymph_%s, 'c');\n",substanceData[i].name);
            break;
        case  'a':
            printf("    printAfferent->PrintSubstance(afferent_%s, 'c');\n",substanceData[i].name);
            break;
        default:
            break;
        } /* switch */
    } /* forLoop */

    exit(1);
}
                                         
VesselSegment::VesselSegment ()
{
    int  i,j ;
    char  ch ;
    static  int  currentType = 0 ;
    static  int  currentNumberOfSubstances = 0 ;
    static  substanceEntry *currentBase = 0;
    static  int  currentNumberOfImmuneCells = 0 ;
    static  immuneCellEntry *currentImmuneBase = 0 ;
    double  immuneQuantity[TOTALSTRAINS];                                                  

    ch = vesselData[vesselIndex].type ;
    plasmaVolume = vesselData[vesselIndex].plasmaVolume;
    totalVolume = vesselData[vesselIndex].totalVolume;
    name = vesselData[vesselIndex].name;

    previousSegment = INDEX_END ;
    nextSegment = INDEX_END ;
    for (i = 0; i < NUMBEROFVESSELS; i++) {
        if (i == vesselIndex) {
            continue;
        } /* if */
        if (ch == vesselData[i].type) {
            if (strcmp(vesselData[i].name, vesselData[vesselIndex].previousName) == 0) {
                previousSegment = i;
            } /* if */
            if (strcmp(vesselData[i].name, vesselData[vesselIndex].nextName) == 0) {
                nextSegment = i;
            } /* if */
        } /* if */
    } /* forLoop */

    if (ch != currentType) {
        currentNumberOfSubstances = 0 ;
        currentBase = 0;
        for (i = 0; i < TOTALSUBSTANCES; i++) {
            if (substanceData[i].type == ch) {
                currentBase = substanceData + i;
                for ( ; i < TOTALSUBSTANCES; i++) {
                    if (substanceData[i].type != ch) {
                        break;
                    } /* if */
                    currentNumberOfSubstances++;
                } /* forLoop */
                break;
            } /* if */
        } /* forLoop */
        if (currentBase == 0) {
            printf("Initializesubstances: can't find type: %c (%s)\n",ch,name);
            // exit(1);       
            currentBase = substanceData ;
        } /* if */    
        currentNumberOfImmuneCells = 0 ;
        currentImmuneBase = 0;
        for (i = 0; i < TOTALIMMUNECELLS; i++) {
            if (immuneCellData[i].type == ch) {
                currentImmuneBase = immuneCellData + i;
                for ( ; i < TOTALIMMUNECELLS; i++) {
                    if (immuneCellData[i].type != ch) {
                        break;
                    } /* if */
                    currentNumberOfImmuneCells++;
                } /* forLoop */
                break;
            } /* if */
        } /* forLoop */
        if (currentImmuneBase == 0) {
            printf("initializeimmuneCells: can't find type: %c (%s)\n",ch,name);
            // exit(1);
            currentImmuneBase = immuneCellData;
        } /* if */    
        currentType = ch ;
    } /* if */
    numberOfSubstances = currentNumberOfSubstances ;
    substanceBase = currentBase;
    substanceQuantity = new  double [numberOfSubstances];
    dSubstanceQuantity = new  double [numberOfSubstances];
 
    transferFlag = 0.0;
    for (i = 0; i < numberOfSubstances; i++) {
        dSubstanceQuantity[i] = 0.0 ;
        substanceQuantity[i] = Concentration2Umoles(substanceBase[i].initialConcentration,i);
    } /* forLoop */                      
                                         
    numberOfImmuneCells = currentNumberOfImmuneCells ;
    immuneCellBase  = currentImmuneBase; 
    immuneCells = new  GenericImmuneCell [numberOfImmuneCells];
    for (i = 0; i < numberOfImmuneCells; i++) {
        for (j = 0; j < TOTALSTRAINS; j++) {
            immuneQuantity[j] = ImmuneConcentration2Umoles(immuneCellBase[i].initialConcentration[j], i);
        } /* jForLoop */     
        immuneCells[i].ResetImmuneCell(immuneQuantity, immuneCellBase[i].initialProfile, immuneCellBase[i].name, name);  
    } /* forLoop */                      
    vesselIndex++;
}

VesselSegment   *VesselSegment::FindVessel (char *s)
{
    int  i;
    char  ch;

    ch =  *s ;
    s += 2;
    for (i = 0; i < NUMBEROFVESSELS; i++) {
        if (ch == vesselData[i].type) {
            if (strcmp(vesselData[i].name, s) == 0) {
                return(this + i) ;
            } /* if */
        } /* if */
    } /* forLoop */
    printf("FindVessel: cannot find:(ch:%c) (s:%s)\n",ch,s);
    exit(1);
    return(0) ;
}


int  VesselSegment::FindSubstanceIndex (char *s)
{
    int  i;
         
    for (i = 0; i < numberOfSubstances; i++) {
        if (strcmp(substanceBase[i].name, s) == 0) {
            return(i) ;
        } /* if */
    } /* forLoop */
    printf("FindSubstanceindex: cannot find: (Substance:%s),substanceBase[0]:%s, Vessel:%s\n",s,substanceBase[0].name,name);
    exit(1);
    return(0) ;
}


double  &VesselSegment::FindSubstance (char *s,char  flag)
{
    int  substanceIndex ;
    substanceIndex = FindSubstanceIndex(s) ;
    return(substanceQuantity[substanceIndex]) ;
}


int  VesselSegment::FindImmuneCellIndex (char *s)
{
    int  i;
                             
    for (i = 0; i < numberOfImmuneCells; i++) {
        if (strcmp(immuneCells[i].ReadName(), s) == 0) {
            return(i) ;
        } /* if */
    } /* forLoop */
    printf("FindImmuneCellIndex: cannot find: (immune cell:%s),immuneCellBase[0]:%s, Vessel:%s\n",s,immuneCellBase[0].name,name);
    exit(1);
    return(0) ;
}


GenericImmuneCell  &VesselSegment::FindImmuneCell (char *s)
{
    int  index ;

    index = FindImmuneCellIndex(s) ;
    return(immuneCells[index]) ;
}



int  VesselSegment::ConnectJunctions (double  dTime)
{
    double  x1;
    int   pointer1 ;
    int  index1;
    int  numberOfBloodVessels = 0;
    VesselSegment *vessels = this;

    for (index1 = 0; index1 < NUMBEROFVESSELS; index1++) {
        if ((vessels[index1].nextSegment < 0) && (vessels[index1].previousSegment < 0)) {
            printf("WARNING: weird segment: %s input and output both turned off\n",vesselData[index1].name);
            continue;
            // exit(1);
        } /* if */

        if (vesselData[index1].type == 'c') {
            numberOfBloodVessels++;
            x1 = dTime * vesselData[index1].flowOut / vesselData[index1].totalVolume ;
        } /* if */
        else {
            x1 = vesselData[index1].flowOut / vesselData[index1].totalVolume ;
        } /* else */
        if (x1 >= .99) {
            // printf("bad time constant out: %s  %g\n",vesselData[index1].name,x1);
            x1 = .99;
        } /* if */
        vessels[index1].timeConstantValueOut = x1;

        x1 = vesselData[index1].flowIn ;
        if (x1 < 0) {     /* not a junction */
            vessels[index1].previousSegment = INDEX_END ;
        } /* if */
        else {
            pointer1 = vessels[index1].previousSegment;
            if (pointer1 < 0) {
                printf("ERROR: invalid junction: no 'previous segment' but FlowIn  > 0:  %s\n",vesselData[index1].name);
                exit(1);
            } /* if */
            x1 *= dTime / vesselData[pointer1].totalVolume ;
            if (x1 >= .99) {
                // printf("bad time constant in: %s  %g\n",vesselData[index1].name,x1);
                x1 = .99;
            } /* if */
            vessels[index1].timeConstantValueIn = x1;
        } /* else */
    } /* forLoop */
    return(numberOfBloodVessels) ;
}


void  VesselSegment::CalculateFlows (int  numberOfBloodVessels)
{
    int   pointer1 ;
    double  timeConstantValueIn,timeConstantValueOut,temp1;
    int  i;
    int  index1;
    VesselSegment *vessels = this ;
    substanceEntry *substanceBase;
    int  numberOfSubstances, numberOfImmuneCells ;
    VesselSegment *destination;
    double   *quantityPointer ;
    double   *dQuantityPointer;

    for (index1 = 0; index1 < numberOfBloodVessels; index1++) {
        pointer1 = vessels[index1].previousSegment;
        if (pointer1 >= 0) {
            substanceBase = vessels[index1].substanceBase;
            timeConstantValueIn = vessels[index1].timeConstantValueIn;
            numberOfSubstances = vessels[index1].numberOfSubstances;
            for (i = 0; i < numberOfSubstances; i++) {
                temp1 = vessels[pointer1].substanceQuantity[i] * timeConstantValueIn ;
                vessels[pointer1].dSubstanceQuantity[i] -=  temp1;
                vessels[index1].dSubstanceQuantity[i]  +=  temp1;
//  printf("p:temp1:%g  from:%s[%s]:%g to:%s[%s]:%g\n",temp1,vesselData[pointer1].name,vessels[pointer1].substanceBase[i].name,vessels[pointer1].dSubstanceQuantity[i],vesselData[index1].name,vessels[index1].substanceBase[i].name,vessels[index1].dSubstanceQuantity[i]);
            } /* forLoop */
        } /* if */

        pointer1 = vessels[index1].nextSegment;
        if (pointer1 >= 0) {
            substanceBase = vessels[index1].substanceBase;
            timeConstantValueOut = vessels[index1].timeConstantValueOut;
            numberOfSubstances = vessels[index1].numberOfSubstances;
            for (i = 0; i < numberOfSubstances; i++) {
                temp1 = timeConstantValueOut * vessels[index1].substanceQuantity[i] ;
                vessels[pointer1].dSubstanceQuantity[i] += temp1;
                vessels[index1].dSubstanceQuantity[i]  -= temp1;
//  printf("n:temp1:%g  from:%s[%s]:%g to:%s[%s]:%g\n",temp1,vesselData[pointer1].name,vessels[pointer1].substanceBase[i].name,vessels[pointer1].dSubstanceQuantity[i],vesselData[index1].name,vessels[index1].substanceBase[i].name,vessels[index1].dSubstanceQuantity[i]);
            } /* forLoop */
        } /* if */
    }

    for (index1 = 0; index1 < numberOfBloodVessels; index1++) {
        destination = vessels + index1;
        numberOfSubstances = destination->numberOfSubstances;
        quantityPointer = destination->substanceQuantity;
        dQuantityPointer = destination->dSubstanceQuantity;
        for (i = 0; i < numberOfSubstances; i++,quantityPointer++,dQuantityPointer++) {
            *quantityPointer +=  *dQuantityPointer;
#if 1
            if (*quantityPointer < 0.0) {
                printf("ERROR Substance<0: %s[%s] %g (dquantity:%g)\n",vesselData[index1].name,destination->substanceBase[i].name, *quantityPointer, *dQuantityPointer);
                exit(1);
            } /* if */
#endif
            *dQuantityPointer = 0.0;
        } /* forLoop */
    }

    for (index1 = numberOfBloodVessels; index1 < NUMBEROFVESSELS; index1++) {
        if (vessels[index1].transferFlag >= 1.0) {
            // printf("transfer name:%s\n",vessels[index1].name);
            pointer1 = vessels[index1].nextSegment;
            if (pointer1 >= 0) {
                timeConstantValueOut = vessels[index1].timeConstantValueOut;
                numberOfSubstances = vessels[index1].numberOfSubstances;
                for (i = 0; i < numberOfSubstances; i++) {   /* assumes vessels properly sorted */
                    temp1 = timeConstantValueOut * vessels[index1].substanceQuantity[i] ;
                    vessels[pointer1].substanceQuantity[i] += temp1;
                    vessels[index1].substanceQuantity[i]  -= temp1;
                } /* forLoop */
                numberOfImmuneCells = vessels[index1].numberOfImmuneCells;
                for (i = 0; i < numberOfImmuneCells; i++) {   /* assumes vessels properly sorted */
                    vessels[index1].immuneCells[i].MigrateOutputWithProfile(vessels[pointer1].immuneCells[i],timeConstantValueOut);
                } /* forLoop */
            } /* if */
            vessels[index1].transferFlag = 0;
        } /* if */
    }
}



void  VesselSegment::Snapshot ()
{
    int  i, j ;
    VesselSegment *vessels = this;
    double  x1,volume;

    printf("Snapshot:VesselSegment\n");

    for (i = 0; i < NUMBEROFVESSELS; i++) {
        printf("%s: transferFlag:%g, numberOfSubstances:%d\n",vessels[i].name,vessels[i].transferFlag,vessels[i].numberOfSubstances);
        for (j = 0; j < vessels[i].numberOfSubstances; j++) {
            volume = vessels[i].ReadVolume(vessels[i].substanceBase[j].whichVolume);
            x1 = vessels[i].substanceQuantity[j] * vessels[i].substanceBase[j].quantityConversionFactor * vessels[i].substanceBase[j].volumeConversionFactor / volume;
            printf(" %s:  (q:%g [%g %s]  dQ:%g)",vessels[i].substanceBase[j].name,vessels[i].substanceQuantity[j],x1,vessels[i].substanceBase[j].concentrationUnits,vessels[i].dSubstanceQuantity[j]);
            printf("\n");
        } /* forLoop */
        for (j = 0; j < vessels[i].numberOfImmuneCells; j++) {
            immuneCells[i].Snapshot() ;
        } /* forLoop */
    } /* forLoop */
    printf("\n");
}

            
void  VesselSegment::PrintSubstance (int  substanceIndex, char  type)
{
    double  x1,volume;
    volume = ReadVolume(substanceBase[substanceIndex].whichVolume);
    x1 = substanceQuantity[substanceIndex] * substanceBase[substanceIndex].quantityConversionFactor;
#if  PLOTFLAG
    switch (type) {
    case  'c':         /* concentration */
        printf("%s.%s: %g\n",name,substanceBase[substanceIndex].name,x1 * substanceBase[substanceIndex].volumeConversionFactor / volume);
        break;
    case  'q':         /* quantity */
        printf("%s.%s: %g\n",name,substanceBase[substanceIndex].name,x1);
        break;
    case  'm':         /* quantity in umoles */
        printf("%s.%s: %g\n",name,substanceBase[substanceIndex].name,substanceQuantity[substanceIndex]);
        break;
    default:
        break;
    } /* switch */
#else
//    printf(" %s: %s: %g %s  (%g %s,  %g umoles)\n",name,substanceBase[substanceIndex].name,x1 * substanceBase[substanceIndex].volumeConversionFactor / volume,substanceBase[substanceIndex].concentrationUnits,x1,substanceBase[substanceIndex].quantityUnits,substanceQuantity[substanceIndex] );
    printf(" %s: %s: %g %s  (%g umoles/mm3,  %g umoles)\n",name,substanceBase[substanceIndex].name,x1 * substanceBase[substanceIndex].volumeConversionFactor / volume,substanceBase[substanceIndex].concentrationUnits,substanceQuantity[substanceIndex] / volume,substanceQuantity[substanceIndex] );
#endif

}


            
void  VesselSegment::PrintImmuneCell (char *s, int  index, int  strainIndex, int  profileIndex, char  type)
{
    double  x2,volume;
    volume = ReadVolume(immuneCellBase[index].whichVolume);
#if  PLOTFLAG
    switch (type) {
    case  't':          /* total */ 
        x2 = immuneCells[index].ReadTotal();
        printf("%s.%s.%s: %g\n",name,immuneCells[index].ReadName(),s,x2 * immuneCellBase[index].quantityConversionFactor * immuneCellBase[index].volumeConversionFactor / volume);
        break;
    case  'p':         /* with profile */
        x2 = immuneCells[index].ReadValueWithProfile(strainIndex,profileIndex);
        printf("%s.%s.%s: %g\n",name,immuneCells[index].ReadName(),s,x2 * immuneCellBase[index].quantityConversionFactor * immuneCellBase[index].volumeConversionFactor / volume);
        break;
    default:
        break;
    } /* switch */
#else                  
    x2 = immuneCells[index].ReadValueWithProfile(strainIndex,profileIndex);
    // printf("x2 :%g %g strainIndex:%d profileIndex:%d\n",x2,immuneCells[index].ReadValue(strainIndex),strainIndex,profileIndex);
    immuneCells[index].Snapshot() ;   /* for now */      
    printf(" %s: %s: %s: %g %s  (%g umoles/mm3,  %g umoles)\n",name,immuneCells[index].ReadName(),s, x2 * immuneCellBase[index].quantityConversionFactor * immuneCellBase[index].volumeConversionFactor / volume,immuneCellBase[index].concentrationUnits, x2 / volume, x2 );
#endif
}                     


void  GenericBody::PrintSubstances (double  temp2)
{
//    static  VesselSegment *printCapillary = vessels->FindVessel("c.hepaticSinusoid") ;
    static  VesselSegment *printCapillary = vessels->FindVessel("c.genericCapillary") ;
    static  VesselSegment *printReservoir = vessels->FindVessel("R.bloodReservoir") ;
    static  VesselSegment *printEfferent =  vessels->FindVessel("l.thoracicDuct5") ;
    static  VesselSegment *printEfferent1 =  vessels->FindVessel("l.thoracicDuct1") ;
    static  VesselSegment *printEfferent2 =  vessels->FindVessel("l.thoracicDuct2") ;
    static  VesselSegment *printEfferent3 =  vessels->FindVessel("l.thoracicDuct3") ;
    static  VesselSegment *printEfferent4 =  vessels->FindVessel("l.thoracicDuct4") ;
    static  VesselSegment *printAfferent =  vessels->FindVessel("a.mediastinalAfferentTest") ;
//    static  VesselSegment *printCapillary = vessels->FindVessel("c.venaCava") ;
//    static  VesselSegment *printCapillary = vessels->FindVessel("c.aorta") ;
//    static  VesselSegment *printCapillary = vessels->FindVessel("c.cerebralCapillary") ;
//    static  VesselSegment *genericCapillary = vessels->FindVessel("c.genericCapillary") ;
//    static  VesselSegment *pituitaryPortal =  vessels->FindVessel("c.hypophysealPortalVein") ;
    static  VesselSegment *glomularCapillary =  vessels->FindVessel("c.glomularCapillary") ;
    static  VesselSegment *hepaticSinusoid = vessels->FindVessel("c.hepaticSinusoid") ;
    static  VesselSegment *venaCava = vessels->FindVessel("c.venaCava") ;
    static  VesselSegment *aorta = vessels->FindVessel("c.aorta") ;
    static  VesselSegment *cerebralCapillary = vessels->FindVessel("c.cerebralCapillary") ;
    static  VesselSegment *pulmonaryCapillary = vessels->FindVessel("c.pulmonaryCapillary") ;
    static  VesselSegment *portalVein = vessels->FindVessel("c.portalVein") ;
    static  VesselSegment *splenicCapillary = vessels->FindVessel("c.splenicCapillary") ;
    static  VesselSegment *thoracicDuct3 =  vessels->FindVessel("l.thoracicDuct3") ;
    static  VesselSegment *thoracicDuct2 =  vessels->FindVessel("l.thoracicDuct2") ;
    static  VesselSegment *thoracicDuct1 =  vessels->FindVessel("l.thoracicDuct1") ;
    static  VesselSegment *commonBileDuct = vessels->FindVessel("b.commonBileDuct") ;
    static  VesselSegment *pancreaticDuct = vessels->FindVessel("b.pancreaticDuct") ;
    static  VesselSegment *stomach = vessels->FindVessel("d.stomach") ;
    static  VesselSegment *smallIntestine = vessels->FindVessel("d.duodenum") ;
    static  VesselSegment *esophagus = vessels->FindVessel("d.esophagus") ;

    static  int  reservoir_bCellNaive  = printReservoir->FindImmuneCellIndex("bCellNaive") ;
    static  int  reservoir_plasmaCell  = printReservoir->FindImmuneCellIndex("plasmaCell") ;
    static  int  reservoir_igM  = printReservoir->FindImmuneCellIndex("igM") ;
    static  int  reservoir_tcEffector  = printReservoir->FindImmuneCellIndex("tcEffector") ;
    static  int  lymphOutput_plasmaCell  = printEfferent->FindImmuneCellIndex("plasmaCell") ;
    static  int  monocyte  = printCapillary->FindSubstanceIndex("monocyte") ;
    static  int  gmcsf  = printCapillary->FindSubstanceIndex("gmcsf") ;
    static  int  il3  = printCapillary->FindSubstanceIndex("il3") ;
    static  int  il5  = printCapillary->FindSubstanceIndex("il5") ;

    static  int  reservoir_bCellMemory  = printReservoir->FindImmuneCellIndex("bCellMemory") ;
    static  int  reservoir_thMemory   = printReservoir->FindImmuneCellIndex("thMemory") ;
    static  int  reservoir_tcMemory   = printReservoir->FindImmuneCellIndex("tcMemory") ;
    static  int  lymphOutput_bCellMemory = printEfferent->FindImmuneCellIndex("bCellMemory") ;
    static  int  lymphOutput_thMemory    = printEfferent->FindImmuneCellIndex("thMemory") ;
    static  int  lymphOutput_tcMemory    = printEfferent->FindImmuneCellIndex("tcMemory") ;
                                        
    static  int  lymphInput_bCellMemory = printAfferent->FindImmuneCellIndex("bCellMemory") ;
    static  int  lymphInput_thMemory    = printAfferent->FindImmuneCellIndex("thMemory") ;
    static  int  lymphInput_tcMemory    = printAfferent->FindImmuneCellIndex("tcMemory") ;

                           

    if (temp2 == 0) {
        printf("; inject\n");
#if 0
        printReservoir->InjectSubstance(reservoir_bCellNaiveRecirculate + 1, 1000.0);   /* inject 1000 cells */
        printf("inject\n");
        genericLymphaticCapillary->InjectSubstance(lymphChylomicrons, 6.25e-2);   /* inject 25000mg = 25grams */
        // printf("feedingTime : %g\n",temp2);
        esophagus->SetSubstanceQuantity(proteinSolid, 33.0);
        esophagus->SetSubstanceQuantity(fats, 17.0);
        esophagus->SetSubstanceQuantity(carbohydrates, 216.0);
    if (temp2 == 60 * 60000) {
        printCapillary->InjectSubstance(trh, 7.0);   /* inject 25ug trh (Greenspan112) */
        printCapillary->InjectSubstance(t3,  0.031);   /* inject  15ug t3 (Greenspan112) */
        printCapillary->InjectSubstance(t4,  0.077);   /* inject  60ug t4 (Greenspan112) */
    } /* if */
    if (temp2 == 240 * 60000) {
        printCapillary->InjectSubstance(trh, 110.0);   /* inject 400ug trh (Greenspan112) */
        printCapillary->InjectSubstance(t3,  0.063);   /* inject  30ug t3 (Greenspan112) */
        printCapillary->InjectSubstance(t4,  0.154);   /* inject  120ug t4 (Greenspan112) */
        printCapillary->InjectSubstance(t3,  0.105);   /* inject  50ug t3 (Berne918) */
        printCapillary->InjectSubstance(t4,  0.257);   /* inject  200ug t4 (berne918) */
        printCapillary->InjectSubstance(t3,  0.031);   /* inject  15ug t3 (Greenspan112) */
        printCapillary->InjectSubstance(t4,  0.077);   /* inject  60ug t4 (Greenspan112) */
    } /* if */
#endif
    } /* if */
#if RUNERRORS
    return;
#endif


#if PLOTFLAG               
    printReservoir->PrintImmuneCell("t", reservoir_bCellMemory, INFLUENZASTRAIN, 0, 't');
    printReservoir->PrintImmuneCell("t", reservoir_thMemory, INFLUENZASTRAIN, 0, 't');
    printReservoir->PrintImmuneCell("t", reservoir_tcMemory, INFLUENZASTRAIN, 0, 't');
                                        
    printEfferent->PrintImmuneCell("t", lymphOutput_bCellMemory, INFLUENZASTRAIN, 0, 't');
    printEfferent->PrintImmuneCell("t", lymphOutput_thMemory, INFLUENZASTRAIN, 0, 't');
    printEfferent->PrintImmuneCell("t", lymphOutput_tcMemory, INFLUENZASTRAIN, 0, 't');
    
    printAfferent->PrintImmuneCell("t", lymphInput_bCellMemory, INFLUENZASTRAIN, 0, 't');
    printAfferent->PrintImmuneCell("t", lymphInput_thMemory, INFLUENZASTRAIN, 0, 't');
    printAfferent->PrintImmuneCell("t", lymphInput_tcMemory, INFLUENZASTRAIN, 0, 't');

    printReservoir->PrintImmuneCell("t", reservoir_tcEffector, INFLUENZASTRAIN, 0, 't');
    printEfferent->PrintImmuneCell("t", lymphOutput_plasmaCell, INFLUENZASTRAIN, IGA, 't');
    printCapillary->PrintSubstance(gmcsf, 'c');
    printCapillary->PrintSubstance(monocyte, 'c');
    printCapillary->PrintSubstance(il3, 'c');
    printCapillary->PrintSubstance(il5, 'c');

/* 
    printf("%g",temp2 /60000.0);
    printf(" %g %g %g %g\n",proteinSolid + proteinChyme,bloodAminoAcids,aminoAcids,peptides);
    printCapillary->PrintSubstance(bloodAminoAcids, 'q');
    printCapillary->PrintSubstance(chylomicrons, 'q');
    printCapillary->PrintSubstance(glucose, 'q');
    printCapillary->PrintSubstance(gastrin, 'c');
    printCapillary->PrintSubstance(cck, 'c');
    printCapillary->PrintSubstance(secretin, 'c');
    stomach->PrintSubstance(hcl, 'c');
    printf("\n");
 */


    return ;
#endif

    printf("\n%g\n",temp2 /60000.0);

#if 1

    printReservoir->PrintImmuneCell("bkgndIgm", reservoir_bCellNaive, BACKGROUNDSTRAIN, IGM, 'c');
    printReservoir->PrintImmuneCell("fluIga", reservoir_plasmaCell, INFLUENZASTRAIN, IGA, 'c');
    printReservoir->PrintImmuneCell("fluIgm", reservoir_igM, INFLUENZASTRAIN, IGM, 'c');
    printReservoir->PrintImmuneCell("bkgndIgm", reservoir_igM, BACKGROUNDSTRAIN, IGM, 'c');
    printEfferent->PrintImmuneCell("fluIga", lymphOutput_plasmaCell, INFLUENZASTRAIN, IGA, 'c');
#endif


#if 0                                                 

    printCapillary->PrintSubstance(glucose, 'c');
    printCapillary->PrintSubstance(insulin, 'c');
    printCapillary->PrintSubstance(glucagon, 'c');


    printCapillary->PrintSubstance(chylomicrons, 'c');
    thoracicDuct3->PrintSubstance(lymphChylomicrons, 'c');
    thoracicDuct2->PrintSubstance(lymphChylomicrons, 'c');
    thoracicDuct1->PrintSubstance(lymphChylomicrons, 'c');
    thoracicDuct5->PrintSubstance(lymphChylomicrons, 'c');
    genericLymphaticCapillary->PrintSubstance(lymphChylomicrons, 'c');
    printCapillary->PrintSubstance(glucose, 'c');
    printCapillary->PrintSubstance(lactate, 'c');
    printCapillary->PrintSubstance(glycerol, 'c');
    printCapillary->PrintSubstance(fattyAcids, 'c');
    printCapillary->PrintSubstance(bloodAminoAcids, 'c');
    printCapillary->PrintSubstance(ketones, 'c');
    printCapillary->PrintSubstance(vldl, 'c');
    printCapillary->PrintSubstance(idl, 'c');
    printCapillary->PrintSubstance(ldl, 'c');
    printCapillary->PrintSubstance(plasmaProteins, 'c');

    printCapillary->PrintSubstance(oxygen, 'c');
    printCapillary->PrintSubstance(CO2, 'c');

    printCapillary->PrintSubstance(insulin, 'c');
    printCapillary->PrintSubstance(glucagon, 'c');

    glomularCapillary->PrintSubstance(trh, 'c');
    pituitaryPortal->PrintSubstance(trh, 'c');
    pituitaryPortal->PrintSubstance(crh, 'c');
    // genericCapillary->PrintSubstance(trh, 'c');
    printCapillary->PrintSubstance(crh, 'c');
    printCapillary->PrintSubstance(acth, 'c');
    printCapillary->PrintSubstance(cortisol, 'c');
    printCapillary->PrintSubstance(trh, 'c');
    printCapillary->PrintSubstance(tsh, 'c');
    printCapillary->PrintSubstance(t4, 'c');
    printCapillary->PrintSubstance(t3, 'c');
    printCapillary->PrintSubstance(insulin, 'c');
    printCapillary->PrintSubstance(glucagon, 'c');
    printCapillary->PrintSubstance(epinephrine, 'c');
    printCapillary->PrintSubstance(lactate, 'c');
    printCapillary->PrintSubstance(glycerol, 'c');
    printCapillary->PrintSubstance(fattyAcids, 'c');
    printCapillary->PrintSubstance(bloodAminoAcids, 'c');
    printCapillary->PrintSubstance(ketones, 'c');
    printCapillary->PrintSubstance(vldl, 'c');
    printCapillary->PrintSubstance(idl, 'c');
    printCapillary->PrintSubstance(ldl, 'c');
    printCapillary->PrintSubstance(plasmaProteins, 'c');
    printCapillary->PrintSubstance(iodine, 'c');
    commonBileDuct->PrintSubstance(bileBileSalts, 'c');
    commonBileDuct->PrintSubstance(bileCholesterol, 'c');
//    esophagus->PrintSubstance(proteinSolid, 'c');

    printCapillary->PrintSubstance(gastrin, 'c');
    printCapillary->PrintSubstance(cck, 'c');
    printCapillary->PrintSubstance(secretin, 'c');
    printCapillary->PrintSubstance(gip, 'c');
    printCapillary->PrintSubstance(insulin, 'c');
    printCapillary->PrintSubstance(somatostatin, 'c');
    printCapillary->PrintSubstance(glucagon, 'c');
    printCapillary->PrintSubstance(bloodAminoAcids, 'c');
    printCapillary->PrintSubstance(chylomicrons, 'c');
    printCapillary->PrintSubstance(glucose, 'c');

    // printf("stomachPeptides: %g\n",stomachPeptides, 'c');
    stomach->PrintSubstance(proteinSolid, 'c');
    stomach->PrintSubstance(proteinChyme, 'c');
    stomach->PrintSubstance(peptides, 'c');
    stomach->PrintSubstance(carbohydrates, 'c');
    stomach->PrintSubstance(fats, 'c');
    stomach->PrintSubstance(pepsin, 'c');
    stomach->PrintSubstance(hcl, 'c');

    smallIntestine->PrintSubstance(proteinSolid, 'c');
    smallIntestine->PrintSubstance(proteinChyme, 'c');
    smallIntestine->PrintSubstance(peptides, 'c');
    smallIntestine->PrintSubstance(aminoAcids, 'c');
    smallIntestine->PrintSubstance(carbohydrates, 'c');
    smallIntestine->PrintSubstance(fats, 'c');
    smallIntestine->PrintSubstance(triglycerides, 'c');
    smallIntestine->PrintSubstance(hcl, 'c');
    smallIntestine->PrintSubstance(aminopeptidase, 'c');

    smallIntestine->PrintSubstance(carboxypeptidase, 'c');
    smallIntestine->PrintSubstance(trypsin, 'c');
    smallIntestine->PrintSubstance(chymotrypsin, 'c');
    smallIntestine->PrintSubstance(lipase, 'c');
    smallIntestine->PrintSubstance(amylase, 'c');
    smallIntestine->PrintSubstance(bileSalts, 'c');
    smallIntestine->PrintSubstance(bicarbonate, 'c');

    commonBileDuct->PrintSubstance(bileCarboxypeptidase, 'c');
    commonBileDuct->PrintSubstance(bileTrypsin, 'c');
    commonBileDuct->PrintSubstance(bileChymotrypsin, 'c');
    commonBileDuct->PrintSubstance(bileLipase, 'c');
    commonBileDuct->PrintSubstance(bileAmylase, 'c');
    commonBileDuct->PrintSubstance(bileBileSalts, 'c');
    commonBileDuct->PrintSubstance(bileBicarbonate, 'c');

    pancreaticDuct->PrintSubstance(bileCarboxypeptidase, 'c');
    pancreaticDuct->PrintSubstance(bileTrypsin, 'c');
    pancreaticDuct->PrintSubstance(bileChymotrypsin, 'c');
    pancreaticDuct->PrintSubstance(bileLipase, 'c');
    pancreaticDuct->PrintSubstance(bileAmylase, 'c');
    pancreaticDuct->PrintSubstance(bileBileSalts, 'c');
    pancreaticDuct->PrintSubstance(bileBicarbonate, 'c');
#endif

}

void  GenericBody::Snapshot (double  temp2)
{
    printf("\nSnapshot: GenericBody: time:%g (snap ver 1.0)\n",temp2);
    vessels->Snapshot();
    PrintValues(1) ;
}



void  GenericBody::PlotValues (double  temp2)
{
    printf("{ %g\n",temp2/ (1000.0 * 60.0 * 60.0 * 24.0) );
    PrintSubstances(temp2);
    laminaProperiaTest->PrintValues (0);
    mesentericTestLymphNode->PrintValues (0);
#if 0             
    bronchialTest->PrintValues (0);
    bronchialLymphNode->PrintValues (0);
    peyersPatchTest->PrintValues (0);
  //  respiratoryTract->PrintValues (0);
#endif            
    printf("}\n");
}
                                     
                          
void  VesselSegment::ExecuteInfusion (int  index)
{
     immuneCells[index].ClearValues();
}                     

                       
void  GenericBody::ExecuteInfusion ()
{
    static  int  infusionCount = 0 ;
    static  int  infusionMaximum = 4 * 7 * 24 * 7200;
    static  int  infusionMaximum1 = 8 * 7 * 24 * 7200;
    static  VesselSegment *thoracicDuct1 = vessels->FindVessel("l.thoracicDuct1");
    static  VesselSegment *thoracicDuct2 = vessels->FindVessel("l.thoracicDuct2");
    static  VesselSegment *thoracicDuct3 = vessels->FindVessel("l.thoracicDuct3");
    static  VesselSegment *thoracicDuct4 = vessels->FindVessel("l.thoracicDuct4");
    static  int  lymph_plasmaCell = thoracicDuct4->FindImmuneCellIndex("plasmaCell") ;

    infusionCount++ ;
    if ((infusionCount == infusionMaximum) || (infusionCount == infusionMaximum1) ) {    /* secondary */ 
        printf("$$$$$$$$$$$$$$$$$$$  secondary infusion (%d)\n",infusionCount);
        fprintf(stderr,"$$$$$$$$$$$$$$$$$$$  secondary infusion (%d)\n",infusionCount);
        bronchialTest->ExecuteInfusion (1);  
#if 0
        bronchialLymphNode->ExecuteInfusion (0);
        spleen->ExecuteInfusion (0);
        liver->ExecuteInfusion (0);
        hepaticLymphNode->ExecuteInfusion (0);
        subcutaneousLymphNode->ExecuteInfusion (0);
        miscellaneousLymphNode->ExecuteInfusion (0);
        mediastinalLymphNode->ExecuteInfusion (0);
        mesentericLymphNode->ExecuteInfusion (0);
        skin->ExecuteInfusion (0);
        miscellaneousTissue->ExecuteInfusion (0);
        respiratoryTract->ExecuteInfusion (0);
        intestines->ExecuteInfusion (0);
        boneMarrow->ExecuteInfusion (0);
        thoracicDuct4->ExecuteInfusion(lymph_plasmaCell);
        thoracicDuct3->ExecuteInfusion(lymph_plasmaCell);
        thoracicDuct2->ExecuteInfusion(lymph_plasmaCell);
        thoracicDuct1->ExecuteInfusion(lymph_plasmaCell);
#endif
    } /* if */                    
}
                       
     
                       
void  GenericBody::PrintValues (int  snapFlag)
{
// snapFlag = 1;             

#if 0             
    laminaProperiaTest->PrintValues (snapFlag);
    mesentericTestLymphNode->PrintValues (snapFlag);
    peyersPatchTest->PrintValues (snapFlag);
    bronchialTest->PrintValues (snapFlag);
    bronchialLymphNode->PrintValues (snapFlag);
//    spleen->PrintValues (snapFlag);
    liver->PrintValues (snapFlag);
    hepaticLymphNode->PrintValues (snapFlag);
    subcutaneousLymphNode->PrintValues (snapFlag);
    miscellaneousLymphNode->PrintValues (snapFlag);
    mediastinalLymphNode->PrintValues (snapFlag);
    mesentericLymphNode->PrintValues (snapFlag);
    skin->PrintValues (snapFlag);
    miscellaneousTissue->PrintValues (snapFlag);
    respiratoryTract->PrintValues (snapFlag);
    intestines->PrintValues (snapFlag);
    boneMarrow->PrintValues (snapFlag);
#endif            

//    otherTissue->PrintValuesTop (snapFlag);
//  adiposeTissue->PrintValues (snapFlag);
//  muscle->PrintValues (snapFlag);
//  brain->PrintValues (snapFlag);
//    lungs->PrintValues (snapFlag);
//  hypothalamus->PrintValues (snapFlag);
//  pituitary->PrintValues (snapFlag);
//  thyroid->PrintValues (snapFlag);
//  adrenal->PrintValues (snapFlag);
//  kidney->PrintValues (snapFlag);
//  pancreas->PrintValues (snapFlag);
}
                       

GenericBody::GenericBody (double  stepTime1,double  maximumTime1,double  plotInterval1)
{
    stepTime = stepTime1;
    maximumTime = maximumTime1;
    plotInterval = plotInterval1;
 
    vessels = new  VesselSegment[NUMBEROFVESSELS] ;
    numberOfBloodVessels = vessels->ConnectJunctions(stepTime) ;
}


void  Simulate (double  stepTime,double  maximumTime,double  plotInterval)
{
    GenericBody  human(stepTime,maximumTime,plotInterval) ;
    printf("; stepTime:%g, maximumTime:%g  plotInterval:%g\n",stepTime,maximumTime,plotInterval);
    human.Run();
}

#if 0
void  hack1 (int  *stuff)
{
    stuff[0] = 5 ;
    stuff[1] = 5 ;

}

void  hack ()
{ 
    int stuff[100];
    hack1(stuff);
}
#endif

 int main(int argc, char **argv)
{
    long  count1,count2;
    double  temp1,temp2;

    if (argc != 4) {
        printf("usage: sub stepTime(msec) maximumTime(min) plotInterval(msec) > resultsFile\n");
        exit(0);
    } /* if */

//  hack();

    temp1 = atof(argv[2]);
    time(&count1);
    Simulate(atof(argv[1]),  temp1  * 60000.0, atof(argv[3]) );
    time(&count2);
    temp2 = (double  )(count2 - count1) / 60.0 ;
    printf("; simulation time: %gmin   actual time:%gmin (ratio:%g)\n",temp1, temp2, temp1 / temp2);
    return(0) ;
}



void  GenericBody::ResetSystem ()
{
}

void  GenericBody::Run ()
{
    int  iStepTime;
    double  temp2;
    double  count_print = 0;
    double  flowConstantLymphJunction = stepTime / ( 20.0 * 60000.0);   /* 20min */
    VesselSegment *emptySegmente = vessels->FindVessel("l.thoracicDuct1");
    VesselSegment *emptySegmenta = vessels->FindVessel("a.miscellaneousAfferent");
    VesselSegment *thoracicDuct1 = vessels->FindVessel("l.thoracicDuct1");
    VesselSegment *thoracicDuct2 = vessels->FindVessel("l.thoracicDuct2");
    VesselSegment *thoracicDuct3 = vessels->FindVessel("l.thoracicDuct3");
    VesselSegment *thoracicDuct4 = vessels->FindVessel("l.thoracicDuct4");

    hepaticLymphNode = new GenericImmuneTissue(     vessels->FindVessel("c.hepaticSinusoid") , vessels->FindVessel("a.hepaticAfferent"), vessels->FindVessel("l.thoracicDuct1") ,  vessels->FindVessel("R.bloodReservoir") ,
     77.0 /* grams */ , 77.0 * 1000.0 /* ul */ , "lymphNode", "hepaticLymphNode", stepTime);
        
    subcutaneousLymphNode = new GenericImmuneTissue(     vessels->FindVessel("c.genericCapillary") , vessels->FindVessel("a.subcutaneousAfferent"), vessels->FindVessel("l.thoracicDuct1") ,  vessels->FindVessel("R.bloodReservoir") ,
     7.0 /* grams */ , 7.0 * 1000.0 /* ul */ , "lymphNode", "subcutaneousLymphNode", stepTime);

    miscellaneousLymphNode = new GenericImmuneTissue(     vessels->FindVessel("c.genericCapillary") , vessels->FindVessel("a.miscellaneousAfferent"), vessels->FindVessel("l.thoracicDuct1") ,  vessels->FindVessel("R.bloodReservoir") ,
     175.0 /* grams */ , 175.0 * 1000.0 /* ul */ , "lymphNode", "miscellaneousLymphNode", stepTime);

    mediastinalLymphNode = new GenericImmuneTissue(     vessels->FindVessel("c.pulmonaryCapillary") , vessels->FindVessel("a.mediastinalAfferent"), vessels->FindVessel("l.thoracicDuct1") ,  vessels->FindVessel("R.bloodReservoir") ,
     168.0 /* grams */ , 168.0 * 1000.0 /* ul */ , "lymphNode", "mediastinalLymphNode", stepTime);

    bronchialLymphNode = new GenericImmuneTissue(     vessels->FindVessel("c.pulmonaryCapillary") , vessels->FindVessel("a.mediastinalAfferentTest"), vessels->FindVessel("l.thoracicDuct1") ,  vessels->FindVessel("R.bloodReservoir") ,
     12.0 /* was.13 grams */ , 12.0 * 1000.0 /* was.13 ul */ , "lymphNode", "bronchialLymphNode", stepTime);

    mesentericLymphNode = new GenericImmuneTissue(     vessels->FindVessel("c.portalVein") , vessels->FindVessel("a.mesentericAfferent"), vessels->FindVessel("l.thoracicDuct1") ,  vessels->FindVessel("R.bloodReservoir") ,
     273.0 /* grams */ , 273.0 * 1000.0 /* ul */ , "lymphNode", "mesentericLymphNode", stepTime);
 
    mesentericTestLymphNode = new GenericImmuneTissue(     vessels->FindVessel("c.portalVein") , vessels->FindVessel("a.mesentericAfferentTest"), vessels->FindVessel("l.thoracicDuct1") ,  vessels->FindVessel("R.bloodReservoir") ,
     30.0 /* grams */ , 30.0 * 1000.0 /* ul */ , "lymphNode", "mesentericTestLymphNode", stepTime);
                         
    peyersPatchTest = new GenericImmuneTissue(     vessels->FindVessel("c.portalVein") , emptySegmenta, vessels->FindVessel("a.mesentericAfferentTest") ,  vessels->FindVessel("R.bloodReservoir") ,
     0.1 /* grams */ , 0.1 * 1000.0 /* ul */ , "lymphNode", "peyersPatchTest", stepTime);
                         
    spleen = new GenericImmuneTissue(     vessels->FindVessel("c.splenicCapillary"), emptySegmenta , emptySegmente ,  vessels->FindVessel("R.bloodReservoir") ,
     150.0 /* grams */ , 150.0 * 1000.0 /* ul */ , "spleen", "spleen" ,stepTime);

    boneMarrow = new GenericImmuneTissue( vessels->FindVessel("c.genericCapillary"), emptySegmenta , emptySegmente,   vessels->FindVessel("R.bloodReservoir") ,
     9.8e3 /* grams */ , 9.8e3 * 1000.0 /* ul */ , "boneMarrow", "boneMarrow" ,stepTime);

    lymphJunction = new GenericImmuneTissue( vessels->FindVessel("c.venaCava"), emptySegmenta , vessels->FindVessel("l.thoracicDuct5"),  vessels->FindVessel("R.bloodReservoir") ,
     0.0 /* grams */ , 0.0 * 1000.0 /* ul */ , "lymphJunction", "lymphJunction" ,stepTime);

    liver = new GenericImmuneTissue(     vessels->FindVessel("c.hepaticSinusoid") , emptySegmenta, vessels->FindVessel("a.hepaticAfferent"),  vessels->FindVessel("R.bloodReservoir") ,
     1600.0 /* grams */ , 1600.0 * 1000.0 /* ul */ , "tissue", "liver", stepTime);
  
    skin = new GenericImmuneTissue(     vessels->FindVessel("c.genericCapillary") , emptySegmenta, vessels->FindVessel("a.subcutaneousAfferent"),  vessels->FindVessel("R.bloodReservoir") ,
     3800.0 /* grams */ , 3800.0 * 1000.0 /* ul */ , "tissue", "skin", stepTime);

    miscellaneousTissue = new GenericImmuneTissue(     vessels->FindVessel("c.genericCapillary") , emptySegmenta, vessels->FindVessel("a.miscellaneousAfferent"),  vessels->FindVessel("R.bloodReservoir") ,
     35000.0 /* grams */ , 26000.0 * 1000.0 /* ul */ , "tissue", "miscellaneousTissue", stepTime);

    respiratoryTract = new GenericImmuneTissue(     vessels->FindVessel("c.pulmonaryCapillary") , emptySegmenta, vessels->FindVessel("a.mediastinalAfferent"),  vessels->FindVessel("R.bloodReservoir") ,
     2000.0 /* grams */ , 2000.0 * 1000.0 /* ul */ , "tissue", "respiratoryTract", stepTime);

    bronchialTest = new GenericImmuneTissue(     vessels->FindVessel("c.pulmonaryCapillary") , emptySegmenta, vessels->FindVessel("a.mediastinalAfferentTest"),  vessels->FindVessel("R.bloodReservoir") ,
     1.5 /* grams */ , 1.5 * 1000.0 /* ul */ , "tissue", "bronchialTest", stepTime);

    intestines = new GenericImmuneTissue(     vessels->FindVessel("c.portalVein") , emptySegmenta, vessels->FindVessel("a.mesentericAfferent"),  vessels->FindVessel("R.bloodReservoir") ,
     4000.0 /* grams */ , 4000.0 * 1000.0 /* ul */ , "tissue", "intestines", stepTime);
                                                                            
    laminaProperiaTest  = new GenericImmuneTissue(     vessels->FindVessel("c.portalVein") , emptySegmenta, vessels->FindVessel("a.mesentericAfferentTest"),  vessels->FindVessel("R.bloodReservoir") ,
     0.1 /* grams */ , 0.1 * 1000.0 /* ul */ , "tissue", "laminaProperiaTest", stepTime);
                                                                            
    lungs = new GenericLungs(vessels->FindVessel("c.pulmonaryCapillary"),2.0e-5, 1.0e10 , "lungs" , stepTime ) ;
//    lymphJunction = new GenericLymphJunction(vessels->FindVessel("l.thoracicDuct3") ,vessels->FindVessel("l.thoracicDuct2") ,vessels->FindVessel("l.thoracicDuct1") ,vessels->FindVessel("l.lymphaticVein"), vessels->FindVessel("l.spleenLymphaticCapillary") , vessels->FindVessel("l.hepaticLymphaticCapillary") , vessels->FindVessel("l.smallIntestineLymphaticCapillary") , vessels->FindVessel("l.genericLymphaticCapillary") , vessels->FindVessel("l.extracellularFluid")  ,vessels->FindVessel("c.venaCava"), lymphaticTime  , "lymphJunction" , stepTime ) ;
    mouth = new GenericMouth( vessels->FindVessel("d.esophagus"),  "mouth" , stepTime ) ;
    esophagus = new GenericEsophagus( vessels->FindVessel("d.esophagus"), stepTime / 5000.0, "esophagus" , stepTime ) ;  /* flowConstant = 15 seconds */
    smallIntestine = new GenericSmallIntestine(vessels->FindVessel("d.duodenum"), vessels->FindVessel("d.jejunum"), vessels->FindVessel("c.portalVein"), "smallIntestine" , stepTime ) ;
    stomach = new GenericStomach(vessels->FindVessel("c.portalVein"), vessels->FindVessel("d.stomach"), stepTime / 20000.0, "stomach" , stepTime ) ;
    kidney = new GenericKidney(vessels->FindVessel("c.glomularCapillary") , "kidney" , stepTime ) ;
    sphincterOfOddi = new GenericSphincterOfOddi(vessels->FindVessel("b.commonBileDuct") ,vessels->FindVessel("b.commonHepaticDuct") ,vessels->FindVessel("b.pancreaticDuct") ,vessels->FindVessel("d.duodenum"), vessels->FindVessel("c.genericCapillary"), stepTime / 7000.0 , "sphincterOfOddi" , stepTime ) ;
    otherTissue = new GenericTissue(vessels->FindVessel("c.genericCapillary") , 4.0e-6, 3.5e12, "otherTissue" , stepTime ) ;
    adiposeTissue = new GenericAdiposeTissue(vessels->FindVessel("c.genericCapillary"), 5.0e-4, 3.95e9, "adiposeTissue" , stepTime ) ;
    muscle = new GenericMuscle(vessels->FindVessel("c.genericCapillary"), 0.116,  250e6,  "muscle" , stepTime ) ;
    brain = new GenericBrain(vessels->FindVessel("c.cerebralCapillary"), 2.2e-5, 1.0e11 , "brain" , stepTime ) ;
    pancreas = new GenericPancreas(vessels->FindVessel("b.pancreaticDuct"), vessels->FindVessel("c.portalVein") , "pancreas", stepTime ) ;
    hypothalamus = new GenericHypothalamus(vessels->FindVessel("c.cerebralCapillary") ,vessels->FindVessel("c.hypophysealPortalVein") , "hypothalamus" , stepTime ) ;
    pituitary = new GenericPituitary(vessels->FindVessel("c.cerebralCapillary") ,vessels->FindVessel("c.hypophysealPortalVein") ,  "pituitary" , stepTime ) ;
    thyroid = new GenericThyroid(vessels->FindVessel("c.genericCapillary") , "thyroid" , stepTime ) ;
    adrenal = new GenericAdrenal(vessels->FindVessel("c.genericCapillary") , "adrenal" , stepTime ) ;
              
// VesselSegment::HelpPrint ();
    ResetSystem();
    iStepTime = (int  )stepTime;
    count_print = 0;
    for (temp2 = 0; temp2 <  maximumTime; temp2 += stepTime) {
        if(temp2 >= count_print){
#if !PLOTFLAG
            PrintSubstances(temp2);
            PrintValues(0);
#else         
            PlotValues(temp2);
#endif
            count_print += plotInterval;
        }
#if 0                     
        mouth->Run();
        esophagus->Run();
        stomach->Run();
        smallIntestine->Run();
        sphincterOfOddi->Run();
        hypothalamus->Run();
        pituitary->Run();
        thyroid->Run();
        adrenal->Run();
        adiposeTissue->Run();
        otherTissue->Run();
        muscle->Run();
        brain->Run();
        lungs->Run();
        kidney->Run();
        pancreas->Run();

#endif        
        liver->ExecuteLiver();
        spleen->ExecuteSpleen();
        hepaticLymphNode->ExecuteLymphNodeGeneral();
        subcutaneousLymphNode->ExecuteLymphNodeGeneral();
        miscellaneousLymphNode->ExecuteLymphNodeGeneral();
        mediastinalLymphNode->ExecuteLymphNodeGeneral();
//        bronchialLymphNode->ExecuteLymphNode();
        mesentericLymphNode->ExecuteLymphNodeGeneral();
        mesentericTestLymphNode->ExecuteLymphNode();
//        peyersPatchTest->ExecutePeyersPatch();
        skin->ExecuteGeneralTissue();
        miscellaneousTissue->ExecuteGeneralTissue();
        respiratoryTract->ExecuteLungs();
  //      bronchialTest->ExecuteBronchialTest();
        intestines->ExecuteGeneralTissue();
        laminaProperiaTest->ExecuteLaminaProperia();
        boneMarrow->ExecuteBoneMarrow();
              
        lymphJunction->ExecuteLymphJunction();
        thoracicDuct4->SetTransferFlag(flowConstantLymphJunction);
        thoracicDuct3->SetTransferFlag(flowConstantLymphJunction);
        thoracicDuct2->SetTransferFlag(flowConstantLymphJunction);
        thoracicDuct1->SetTransferFlag(flowConstantLymphJunction);
               
        vessels->CalculateFlows(numberOfBloodVessels);
        ExecuteInfusion();
    }
//    Snapshot(temp2);
}


void  GenericStomach::Run ()
{
    double  rate,x1 ;

    /* hack: [proteinSolid] + 20?[hcl] -> [proteinChyme]  */
    rate = kProteinChyme * proteinSolid * hcl;
    proteinSolid -= rate  * hclMultiplier;
    // printf("Stomach hcl:%g  rate:%g  proteinSolid:%g\n",hcl,rate,proteinSolid);
    hcl -= rate  ;
    proteinChyme += rate * hclMultiplier;

    /* hack... gastrin -> hcl */
    rate = k2Hcl * gastrin + kmHcl;
    // printf("Stomach hcl:%g  rate:%g  gastrin:%g\n",hcl,rate,gastrin);
    if (rate >= 0.0) {
        hcl += rate;
    } /* if */

    /* gastrin -> pepsin */ 
    rate = k2Pepsin * gastrin / (kmPepsin + gastrin) ;
    pepsin += rate;

    /* [protein] + [pepsin] -> 10[peptides] */
    rate = k2Peptides * pepsin * proteinSolid / (kmPeptides + proteinSolid) ;
    proteinSolid -= rate ;
    peptides += 10 * rate;
    // stomachPeptides += 10 * rate;
    rate = k2Peptides * pepsin * proteinChyme / (kmPeptides + proteinChyme) ;
    proteinChyme -= rate ;
    peptides += 10 * rate;
    // stomachPeptides += 10 * rate;

    /* protein,hcl -> gastrin */
    x1 = proteinSolid + proteinChyme ;
    rate = (k2Gastrin * x1 / (kmGastrin + x1)) * (1.0 / (1.0 + kmiGastrin * hcl)) + kbGastrin;
    gastrin += rate;

    /* hack... stomach -> smallIntestine:  3ml/contraction, contraction ~20 seconds */
    /* 3ml/contraction, ~20seconds/contraction, protein halfLife = 90 minutes */
    intestine->SetTransferFlag(flowConstant);
    if (intestine->ReadTransferFlag() >= 1.0) {
        x1 = proteinSolid + proteinChyme + carbohydrates + fats ;
        rate = (1.0 - kStomach2SmallIntestine) * x1 / (1.0e-6 + x1) + kStomach2SmallIntestine;
        x1 = (1.0 / (1.0 + kiStomach2SmallIntestine * smallIntestineNerve.ReadNerve() )) ;
        intestine->SetTimeConstant(initialTimeConstantValueOut * rate * x1);
        // printf("time constant:%g  dhcl:%g   HCL:%g\n",(initialTimeConstantValueOut * rate * x1),hcl * (initialTimeConstantValueOut * rate * x1),hcl);
    } /* if */
}



void  GenericSmallIntestine::Run ()
{
    double  rate ;
    double  x1;

    /* (hack for now) Enterohepatic Circulation, bileSalts ->bloodBileSalts */
    rate = 42.7;
//    bileSalts -= rate ;
    bloodBileSalts += rate;

    /* [protein] ->trypsin-> 10[peptides] */
    rate = k2Peptides * trypsin * proteinSolid / (kmPeptides + proteinSolid) ;
    proteinSolid -= rate ;
    peptides += 10 * rate;

    /* [protein] ->trypsin-> 10[peptides] */
    rate = k2Peptides * chymotrypsin * proteinChyme / (kmPeptides + proteinChyme) ;
    proteinChyme -= rate ;
    peptides += 10 * rate;

    /* [peptides] ->carboxypeptidase|aminopeptidase-> 10[aminoAcids] */
    rate = ( peptides / (kmAminoAcids + peptides)) * (k2AminoAcids * aminopeptidase + k2cAminoAcids * carboxypeptidase) ;
    peptides -= rate ;
    aminoAcids += 10 * rate;

    /* [fats] ->bileSalts-> 100[triglycerides] */
    rate = k2Triglycerides * bileSalts * fats / (kmTriglycerides + fats) ;
    fats -= rate ;
    triglycerides += 100 * rate;

    /* [cck] -> [aminopeptidase] */
    rate = k2Aminopeptidase * cck / (kmAminopeptidase + cck) ;
    aminopeptidase += rate;

    /* hack... [hcl] + [bicarbonate] -> neutralized */
    rate = k2Hcl * hcl * bicarbonate;
    // printf("smallIntestine hcl:%g  rate:%g  bicarbonate:%g\n",hcl,rate,bicarbonate);
    bicarbonate -= rate ;
    hcl -= rate ;
    if (hcl  < 0.0) {
        hcl = 0.0;
    } /* if */

    /* [aminoAcids] ->aminopeptidase-> [bloodAminoAcids] */
    rate = k2BloodAminoAcids * aminopeptidase * aminoAcids / (kmBloodAminoAcids + aminoAcids) ;
    aminoAcids -= rate ;
    bloodAminoAcids += rate;

    /* hack... aminoAcids,peptides,triglycerides -> cck */
    x1 = aminoAcids + peptides * 10.0 ;
    rate = k2Cck  * ( (x1/(kmcck + x1)) + (triglycerides/(kmfcck + triglycerides)) ) + kbcck;
    cck += rate;

    /* carbohydrates,fats -> gip */
    rate = k2Gip * ( (carbohydrates / (kmGip + carbohydrates)) + (fats / (kmfGip + fats)) ) + kbGip;
    gip += rate;

    /* [hcl] -> [secretin] */
    rate = (k2Secretin * hcl / (kmSecretin + hcl))  ;
    //     printf("smallIntestine secretin rate: %g, hcl:%g\n",rate,hcl);
    secretin += rate;

    /* 100[triglycerides] ->lipase-> [chylomicrons] */
    rate = k2Chylomicrons * lipase * triglycerides / (kmChylomicrons + triglycerides) ;
    triglycerides -= rate ;
    chylomicrons += 0.01 * rate;

    /* [carbohydrates] ->amylase-> 100[glucose] */
    rate = k2Glucose * amylase * carbohydrates / (kmGlucose + carbohydrates) ;
    carbohydrates -= rate ;
    glucose += 100.0 * rate;

    /* hack: stomach -> smallIntestine */
    smallIntestineNerve.SetNerve((fats + proteinSolid + proteinChyme)) ;
    // printf("rate:%g, x1:%g  fats:%g protein:%g \n",rate,x1,fats,proteinSolid + proteinChyme);

}



void  GenericMouth::Run ()
{
}


void  GenericEsophagus::Run ()
{
    intestine->SetTransferFlag(flowConstant);
}


void  GenericSphincterOfOddi::Run ()
{
    double  rate,timeConstantValueOut ;

    pancreaticDuct->SetTransferFlag(flowConstant);
    commonHepaticDuct->SetTransferFlag(flowConstant);
    if (pancreaticDuct->ReadTransferFlag() >= 1.0) {
        rate = k2SphincterOfOddi * cck / (kmSphincterOfOddi + cck) ;
        timeConstantValueOut = initialTimeConstantValueOut * rate;
// printf("rate:%g  cck%g  timeConstantValueOut:%g  transferflag:%g\n",rate,cck,timeConstantValueOut,pancreaticDuct->ReadTransferFlag());
        pancreaticDuct->SetTimeConstant(timeConstantValueOut);
        commonHepaticDuct->SetTimeConstant(timeConstantValueOut);

        rate = bileCarboxypeptidase * timeConstantValueOut ;
        bileCarboxypeptidase -= rate;
        carboxypeptidase += rate;

        rate = bileTrypsin * timeConstantValueOut ;
        bileTrypsin -= rate;
        trypsin += rate;

        rate = bileChymotrypsin * timeConstantValueOut ;
        bileChymotrypsin -= rate;
        chymotrypsin += rate;

        rate = bileBileSalts * timeConstantValueOut ;
        bileBileSalts -= rate;
        bileSalts += rate;

        rate = bileBicarbonate * timeConstantValueOut ;
        bileBicarbonate -= rate;
        bicarbonate += rate;

        rate = bileLipase * timeConstantValueOut ;
        bileLipase -= rate;
        lipase += rate;

        rate = bileAmylase * timeConstantValueOut ;
        bileAmylase -= rate;
        amylase += rate;
    } /* if */
}



void  GenericHypothalamus::Run ()
{
    double  rate;

    /* t3 -> trh  rate=1.0e-4/tick */
    rate = k2Trh / (1.0 + kiTrh * t3);
    trh += rate ;
    if (printFlag) {
     printf(" %s: t3->trh rate (1.0e-4): %g\n",organName,rate);
    } /* if */

    /* cortisol,acth -> crh  rate=1.15e-8/tick */
    rate = k2Crh /( (1.0 + ki1Crh * acth) * (1.0 + ki2Crh * cortisol) );
    crh += rate ;
    if (printFlag) {
     printf(" %s: acth->crh rate (1.16e-8): %g\n",organName,rate);
      printFlag = 0;
    } /* if */
}
  

void  GenericPituitary::Run ()
{
    double  rate,x1,x2;

    /* trh -> tsh  rate=.6/tick */
    x1 = trh * trh;
    x2 = t3 * t3 * t3;
//    x1 = trh;
    rate = k2Tsh * (x1 / (kaTsh + x1)) * (1.0 / (1.0 + kiTsh * x2));
    tsh += rate ;
    internalTsh -= rate ;
    internalTsh += rate ;     /* ?  For now */

    if (printFlag) {
       printf("trh:%g  t3:%g  k2:%g  ka:%g  ki:%g  x1:%g  x2:%g\n",trh,t3,k2Tsh,kaTsh,kiTsh,x1,x2);
      printf(" %s: trh->tsh rate (.6): %g\n",organName,rate);
    } /* if */

    /* crh -> acth  rate=3.45e-8/tick */
    rate = k2Acth * crh / (kmActh + crh);
    acth += rate ;
    if (printFlag) {
       printf("crh:%g  k2:%g(exp:6.9e-8)  km:%g(exp:6.66e-10)\n",crh,k2Acth,kmActh);
     printf(" %s: crh->acth rate (3.46e-8): %g\n",organName,rate);
    } /* if */

    printFlag = 0;
}


void  GenericThyroid::PrintValues ()
{
    printf(" thyroid: internalIodine: %g\n",internalIodine);
 printFlag = 1;
}


void  GenericThyroid::Run ()
{
    double  rate;

    /* tsh -> t4,t3  rate=6.7e-7/tick */
    rate = k2T4 * tsh / (kaT4 + tsh) *  (internalIodine / (kmT4 + internalIodine)) ;
    t4 += rate ;
    t3 += rate  * .12 ;
    internalIodine -= rate * 5.0 ;
    if (printFlag) {
     printf(" %s: tsh->t4,t3 rate (6.7e-7): %g\n",organName,rate);
    } /* if */

    /* iodine ->internalIodine   rate=3.4e-6/tick */
    rate = k2Iodine * iodine / (kmIodine + iodine);
    internalIodine += rate ;
    iodine -= rate ;
    if (printFlag) {
     printf(" %s: iodine->internalIodine rate (3.4e-6): %g\n",organName,rate);
      printFlag = 0;
    } /* if */

}



void  GenericAdrenal::Run ()
{
    double  rate;

    /* acth -> cortisol  rate=1.08e-4/tick */
    rate = k2Cortisol * acth / (kmCortisol + acth);
    cortisol += rate ;
    if (printFlag) {
     printf(" %s: acth->cortisol rate (1.08e-4): %g\n",organName,rate);
      printFlag = 0;
    } /* if */

}

void  GenericKidney::Run ()
{
    double  rate;

    /* ------------------ hack clearance equations for now -------------------------- */

    rate = kGastrin * gastrin ;
    gastrin -= rate;

    rate = kcck * cck ;
    // printf("cck rate: %g\n",rate);
    cck -= rate;

    rate = kSecretin * secretin ;
    secretin -= rate;
  //   printf("Liver secretin rate: %g\n",rate);

    rate = kGip * gip ;
    gip -= rate;
    // printf("gip rate: %g\n",rate);

    rate = kInsulin * insulin ;
    insulin -= rate;
    if (printFlag) {
       printf(" %s: insulin: %g\n",organName,rate);
    } /* if */

    rate = kSomatostatin * somatostatin ;
    somatostatin -= rate;
//    printf("somatostatin rate: %g\n",rate);

    rate = kGlucagon * glucagon ;
    glucagon -= rate;
    if (printFlag) {
       printf(" %s: glucagon: %g\n",organName,rate);
    } /* if */

    rate = kT4 * t4 ;
    t4 -= rate;

    rate = kT3 * t3 ;
    t3 -= rate;

    rate = kTsh * tsh ;
    tsh -= rate;

    rate = kTrh * trh ;
    trh -= rate;
    if (printFlag) {
       printf(" %s: trh (1.0e-4): %g\n",organName,rate);
    } /* if */

    rate = kIodine * iodine ;
    iodine -= rate;

    rate = kCrh * crh ;
    crh -= rate;

    rate = kActh * acth ;
    acth -= rate;

    rate = kCortisol * cortisol ;
    cortisol -= rate;

    printFlag = 0;
}



void  GenericPancreas::Run ()
{
    double  rate,x1 ;


//    rate = k2Glucagon;
  //  glucagon += rate;
// return;
    /* [glucose] -> [insulin] */
    x1 = glucose * kmInsulin ;
    x1 = x1 * x1 ;
    x1 = x1 * x1 ;
    rate = k2Insulin * x1 / (1.0 + x1) + kbInsulin ;
    insulin += rate;
    if (printFlag) {
     printf(" %s: insulin rate: %g\n",organName,rate);
    } /* if */

    /* [glucose] -> [glucagon] */
    x1 = glucose *  kmGlucagon;
    x1 = x1 * x1 ;
    x1 = x1 * x1 ;
    rate = k2Glucagon  / (1.0 + x1) ;
    glucagon += rate;
    if (printFlag) {
     printf(" %s: glucagon rate: %g\n",organName,rate);
    } /* if */

#if 0
    /* [glucose] -> [somatostatin] */
    rate = k2Somatostatin * glucose / (kmSomatostatin + glucose) ;
    somatostatin += rate;

    /* hack... [secretin] -> [bicarbonate] */
    rate = k2Bicarbonate * secretin + kmBicarbonate ;
    if (rate < 0.0) {
        rate = 0.0;
    } /* if */
    bicarbonate += rate;

    /* [cck] -> [trypsin] */
    rate = k2Trypsin * cck / (kmTrypsin + cck) ;
    trypsin += rate;

    /* [cck] -> [chymotrypsin] */
    rate = k2Chymotrypsin * cck / (kmChymotrypsin + cck) ;
    chymotrypsin += rate;

    /* [cck] -> [carboxypeptidase] */
    rate = k2Carboxypeptidase * cck / (kmCarboxypeptidase + cck) ;
    carboxypeptidase += rate;

    /* [cck] -> [lipase] */
    rate = k2Lipase * cck / (kmLipase + cck) ;
    lipase += rate;

    /* [cck] -> [amylase] */
    rate = k2Amylase * cck / (kmAmylase + cck) ;
    amylase += rate;
#endif
    printFlag = 0;
}


void  GenericOrgan::ResetGenericOrgan()
{
    glucose6Phosphate = 83.0e-6 * cellVolume ;
    gap = 157.0e-6 * cellVolume ;
    pyruvate = 51.0e-6 * cellVolume;
    acetylCoenzymeA = 39.0e-6 * cellVolume ;
    atp = 1850.0e-6 * cellVolume ;
    adp = 138.0e-6 * cellVolume ;
    malonylCoA = 0.0;                           /* total hack, for beta oxidation control */
    fad = 72.0e-6 * cellVolume ;
    fadh = 180.0e-6 * cellVolume ;
    nad = 72.0e-6 * cellVolume ;
    nadh = 180.0e-6 * cellVolume ;

    hexokinase = 1.0e-6 * cellVolume;
    phosphofructokinase = 5.0e-6 * cellVolume;
    pyruvateKinase = 0.2e-6 * cellVolume;
    pyruvateDehydrogenase = 0.1e-6 * cellVolume;
    isocitrateDehydrogenase = 0.5e-6 * cellVolume;
    atpSynthase = 0.1e-6 * cellVolume;
    atpAse = 1.0e-6 * cellVolume;

    glycogen = 0.0;
    protein = 0.0;
    triglycerides =  0.0;
    cholesterol = 0.0;
    internalFattyAcids = 0.0;
    internalAminoAcids = 0.0;

    printFlag = 0;
}


void  GenericOrgan::PrintValues (int  snapFlag)
{
 return;
    printf(" %s: glucose6Phosphate: %g\n",organName,glucose6Phosphate);
    printf(" %s: gap: %g\n",organName,gap);
    printf(" %s: pyruvate: %g\n",organName,pyruvate);
    printf(" %s: acetylCoenzymeA: %g\n",organName,acetylCoenzymeA);
    printf(" %s: atp: %g\n",organName,atp);
    printf(" %s: adp: %g\n",organName,adp);
    printf(" %s: nad : %g\n",organName,nad );
    printf(" %s: nadh: %g\n",organName,nadh);
    printf(" %s: fad : %g\n",organName,fad );
    printf(" %s: fadh: %g\n",organName,fadh);
    printf(" %s: glycogen: %g\n",organName,glycogen);
    printf(" %s: internalFattyAcids: %g\n",organName,internalFattyAcids);
    printf(" %s: triglycerides: %g\n",organName,triglycerides);
    printf(" %s: protein: %g\n",organName,protein);
    printf(" %s: malonylCoA: %g\n",organName,malonylCoA);
    printFlag = 1;
}



void  GenericBrain::Run ()
{
    EvaluateHexokinase() ;
    EvaluatePhosphofructokinase () ;
    EvaluatePyruvateKinase() ;
    EvaluatePyruvateDehydrogenase () ;
    EvaluateIsocitrateDehydrogenase () ;
    EvaluateAtpSynthase () ;
    EvaluateAtpAse () ;
    #if  METABOLISMDEBUG
        printFlag = 0;
    #endif
}


void  GenericLungs::Run ()
{
    oxygen += 24.0 ;
    CO2 -= 24.0;
//    glucose += 4.0;
//    glucose += 4.4;
    #if  METABOLISMDEBUG
        printFlag = 0;
    #endif
}



void  GenericMuscle::Run ()
{
    glucose -= glucose * 3.9e-3 / 2.0 ;
    fattyAcids -= fattyAcids * 0.16 / 2.0 ;
    lactate += 3.88 / 2.0 ;
    aminoAcids += 30.0 / 2.0 ;
    aminoAcids -= aminoAcids * .113 / 2.0 ;
    plasmaProteins -= plasmaProteins * 3.2e-5 / 2.0;
    #if  METABOLISMDEBUG
        printFlag = 0;
    #endif
}

#if 0
void  GenericLiver::Run ()
{
    double  rate;
    kupffer.ExecuteKupffer();
  return ;
    glucose += 12.84 / 2.0 ;
    fattyAcids -= fattyAcids * 3.56e-2 / 2.0 ;
    vldl += 2.32e-5 / 2.0 ;
    rate = idl * 1.8e-2 / 2.0 ;
    idl -= 2.0 * rate ;
    ldl += rate ;
    ldl -= ldl * 3.27e-4 / 2.0 ;
    lactate -= lactate * 6.6e-2 / 2.0 ;
    aminoAcids -= aminoAcids * 2.97e-2 / 2.0 ;
    glycerol -= glycerol * .52 / 2.0 ;
//    glycerol -= glycerol * .99;
    ketones += .1044 / 2.0 ;
    plasmaProteins += 3.46e-3 / 2.0;
    #if  METABOLISMDEBUG
        printFlag = 0;
    #endif
}
#endif


void  GenericAdiposeTissue::Run ()
{
    double  rate;
    glucose -= glucose * 8.5e-4 / 2.0 ;
    fattyAcids += 4.6 / 2.0 ;
    rate = vldl * 1.78e-2 / 2.0 ;
    vldl -= rate;
    ldl += rate ;
    glycerol += 1.5 / 2.0;
    #if  METABOLISMDEBUG
        printFlag = 0;
    #endif
}


void  GenericTissue::Run ()
{
    glucose -= glucose * 8.6e-3 / 2.0 ;
    fattyAcids -= fattyAcids * .11 / 2.0 ;
    ldl -= ldl * 1.24e-4 / 2.0 ;
    ketones -= ketones * 5.3e-2 / 2.0;
    #if  METABOLISMDEBUG
        printFlag = 0;
    #endif
}



void  GenericImmuneTissue::PrintValues (int  snapFlag)
{
    double  rate;
    int  i;
                                                                                
#if PLOTFLAG                
#if 0 
    printf("%s.%s.a: %g\n",organName,mastCell.ReadName(),mastCell.ReadValueWithProfile(RYEGRASSSTRAIN,IGA));
    printf("%s.%s.m: %g\n",organName,mastCell.ReadName(),mastCell.ReadValueWithProfile(RYEGRASSSTRAIN,IGM));
    printf("%s.%s.g: %g\n",organName,mastCell.ReadName(),mastCell.ReadValueWithProfile(RYEGRASSSTRAIN,IGG));
    printf("%s.%s.e: %g\n",organName,mastCell.ReadName(),mastCell.ReadValueWithProfile(RYEGRASSSTRAIN,IGE));
    printf("%s.%s.a: %g\n",organName,mastCellDegranulate.ReadName(),mastCellDegranulate.ReadValueWithProfile(RYEGRASSSTRAIN,IGA));
    printf("%s.%s.m: %g\n",organName,mastCellDegranulate.ReadName(),mastCellDegranulate.ReadValueWithProfile(RYEGRASSSTRAIN,IGM));
    printf("%s.%s.g: %g\n",organName,mastCellDegranulate.ReadName(),mastCellDegranulate.ReadValueWithProfile(RYEGRASSSTRAIN,IGG));
    printf("%s.%s.e: %g\n",organName,mastCellDegranulate.ReadName(),mastCellDegranulate.ReadValueWithProfile(RYEGRASSSTRAIN,IGE));
    printf("%s.%s.a: %g\n",organName,plasmaCell.ReadName(),plasmaCell.ReadValueWithProfile(RYEGRASSSTRAIN,IGA));
    printf("%s.%s.m: %g\n",organName,plasmaCell.ReadName(),plasmaCell.ReadValueWithProfile(RYEGRASSSTRAIN,IGM));
    printf("%s.%s.g: %g\n",organName,plasmaCell.ReadName(),plasmaCell.ReadValueWithProfile(RYEGRASSSTRAIN,IGG));
    printf("%s.%s.e: %g\n",organName,plasmaCell.ReadName(),plasmaCell.ReadValueWithProfile(RYEGRASSSTRAIN,IGE));
    printf("%s.%s.a: %g\n",organName,bCellMemory.ReadName(),bCellMemory.ReadValueWithProfile(RYEGRASSSTRAIN,IGA));
    printf("%s.%s.m: %g\n",organName,bCellMemory.ReadName(),bCellMemory.ReadValueWithProfile(RYEGRASSSTRAIN,IGM));
    printf("%s.%s.g: %g\n",organName,bCellMemory.ReadName(),bCellMemory.ReadValueWithProfile(RYEGRASSSTRAIN,IGG));
    printf("%s.%s.e: %g\n",organName,bCellMemory.ReadName(),bCellMemory.ReadValueWithProfile(RYEGRASSSTRAIN,IGE));
    printf("%s.%s.1: %g\n",organName,thEffector.ReadName(),thEffector.ReadValueWithProfile(RYEGRASSSTRAIN,TH1));
    printf("%s.%s.2: %g\n",organName,thEffector.ReadName(),thEffector.ReadValueWithProfile(RYEGRASSSTRAIN,TH2));
    printf("%s.%s.0: %g\n",organName,thEffector.ReadName(),thEffector.ReadValueWithProfile(RYEGRASSSTRAIN,TH0));
    printf("%s.%s.1: %g\n",organName,thMemory.ReadName(),thMemory.ReadValueWithProfile(RYEGRASSSTRAIN,TH1));
    printf("%s.%s.2: %g\n",organName,thMemory.ReadName(),thMemory.ReadValueWithProfile(RYEGRASSSTRAIN,TH2));
    printf("%s.%s.0: %g\n",organName,thMemory.ReadName(),thMemory.ReadValueWithProfile(RYEGRASSSTRAIN,TH0));
    printf("%s.%s.1: %g\n",organName,thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ReadName(),thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ReadValueWithProfile(RYEGRASSSTRAIN,TH1));
    printf("%s.%s.2: %g\n",organName,thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ReadName(),thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ReadValueWithProfile(RYEGRASSSTRAIN,TH2));
    printf("%s.%s.0: %g\n",organName,thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ReadName(),thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ReadValueWithProfile(RYEGRASSSTRAIN,TH0));
    printf("%s.%s.12: %g\n",organName,dendriticApc.ReadName(),dendriticApc.ReadValueWithProfile(RYEGRASSSTRAIN,D_IL12));
    printf("%s.%s.10: %g\n",organName,dendriticApc.ReadName(),dendriticApc.ReadValueWithProfile(RYEGRASSSTRAIN,D_IL10));
    printf("%s.%s.rye: %g\n",organName,dendriticApc.ReadName(),dendriticApc.ReadValue(RYEGRASSSTRAIN));
    printf("%s.il3inflammatoryRate: %g\n",organName,il3inflammatoryRate);
    printf("%s.il5inflammatoryRate: %g\n",organName,il5inflammatoryRate);
    printf("%s.%s: %g\n",organName,ige.ReadName(),ige.ReadTotal());
    printf("%s.mastCellNaive: %g\n",organName,mastCellNaive        );
    printf("%s.eosinophil: %g\n",organName,eosinophil        );
    printf("%s.fev1: %g\n",organName,fev1        );
    printf("%s.histamine: %g\n",organName,histamine/( epitheliumvolume/ 1000.0)  * 111.0e3 ); /* umole/Milliliter */ 
    printf("%s.ltc4: %g\n",organName,ltc4     /( epitheliumvolume/ 1000.0) * 625.0e6 ); /* umole/Milliliter */ 
    printf("%s.il3: %g\n",organName,il3      /( epitheliumvolume/ 1000.0) * 1.8e7 ); /* ng/Milliliter */ 
    printf("%s.il5: %g\n",organName,il5      /( epitheliumvolume/ 1000.0) * 3.0e7 ); /* Ng/Milliliter */ 
    printf("%s.il5raw: %g\n",organName,il5   );
#endif
#if 1 
    printf("%s.%s.a: %g\n",organName,plasmaCell.ReadName(),plasmaCell.ReadValueWithProfile(INFLUENZASTRAIN,IGA));
    printf("%s.%s.m: %g\n",organName,plasmaCell.ReadName(),plasmaCell.ReadValueWithProfile(INFLUENZASTRAIN,IGM));
    printf("%s.%s.g: %g\n",organName,plasmaCell.ReadName(),plasmaCell.ReadValueWithProfile(INFLUENZASTRAIN,IGG));
    printf("%s.%s.e: %g\n",organName,plasmaCell.ReadName(),plasmaCell.ReadValueWithProfile(INFLUENZASTRAIN,IGE));
    printf("%s.%s.a: %g\n",organName,bCellMemory.ReadName(),bCellMemory.ReadValueWithProfile(INFLUENZASTRAIN,IGA));
    printf("%s.%s.m: %g\n",organName,bCellMemory.ReadName(),bCellMemory.ReadValueWithProfile(INFLUENZASTRAIN,IGM));
    printf("%s.%s.g: %g\n",organName,bCellMemory.ReadName(),bCellMemory.ReadValueWithProfile(INFLUENZASTRAIN,IGG));
    printf("%s.%s.e: %g\n",organName,bCellMemory.ReadName(),bCellMemory.ReadValueWithProfile(INFLUENZASTRAIN,IGE));
    printf("%s.%s.1: %g\n",organName,thEffector.ReadName(),thEffector.ReadValueWithProfile(INFLUENZASTRAIN,TH1));
    printf("%s.%s.2: %g\n",organName,thEffector.ReadName(),thEffector.ReadValueWithProfile(INFLUENZASTRAIN,TH2));
    printf("%s.%s.0: %g\n",organName,thEffector.ReadName(),thEffector.ReadValueWithProfile(INFLUENZASTRAIN,TH0));
    printf("%s.%s.1: %g\n",organName,thMemory.ReadName(),thMemory.ReadValueWithProfile(INFLUENZASTRAIN,TH1));
    printf("%s.%s.2: %g\n",organName,thMemory.ReadName(),thMemory.ReadValueWithProfile(INFLUENZASTRAIN,TH2));
    printf("%s.%s.0: %g\n",organName,thMemory.ReadName(),thMemory.ReadValueWithProfile(INFLUENZASTRAIN,TH0));
    printf("%s.%s.a: %g\n",organName,bCellMemoryMarginal.ReadName(),bCellMemoryMarginal.ReadValueWithProfile(INFLUENZASTRAIN,IGA));
    printf("%s.%s.m: %g\n",organName,bCellMemoryMarginal.ReadName(),bCellMemoryMarginal.ReadValueWithProfile(INFLUENZASTRAIN,IGM));
    printf("%s.%s.g: %g\n",organName,bCellMemoryMarginal.ReadName(),bCellMemoryMarginal.ReadValueWithProfile(INFLUENZASTRAIN,IGG));
    printf("%s.%s.e: %g\n",organName,bCellMemoryMarginal.ReadName(),bCellMemoryMarginal.ReadValueWithProfile(INFLUENZASTRAIN,IGE));
#endif
#if 0 
    printf("%s.%s.1: %g\n",organName,thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ReadName(),thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ReadValueWithProfile(INFLUENZASTRAIN,TH1));
    printf("%s.%s.2: %g\n",organName,thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ReadName(),thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ReadValueWithProfile(INFLUENZASTRAIN,TH2));
    printf("%s.%s.0: %g\n",organName,thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ReadName(),thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ReadValueWithProfile(INFLUENZASTRAIN,TH0));
    printf("%s.%s.a: %g\n",organName,mastCell.ReadName(),mastCell.ReadValueWithProfile(INFLUENZASTRAIN,IGA));
    printf("%s.%s.m: %g\n",organName,mastCell.ReadName(),mastCell.ReadValueWithProfile(INFLUENZASTRAIN,IGM));
    printf("%s.%s.g: %g\n",organName,mastCell.ReadName(),mastCell.ReadValueWithProfile(INFLUENZASTRAIN,IGG));
    printf("%s.%s.e: %g\n",organName,mastCell.ReadName(),mastCell.ReadValueWithProfile(INFLUENZASTRAIN,IGE));
    printf("%s.%s.a: %g\n",organName,mastCellDegranulate.ReadName(),mastCellDegranulate.ReadValueWithProfile(INFLUENZASTRAIN,IGA));
    printf("%s.%s.m: %g\n",organName,mastCellDegranulate.ReadName(),mastCellDegranulate.ReadValueWithProfile(INFLUENZASTRAIN,IGM));
    printf("%s.%s.g: %g\n",organName,mastCellDegranulate.ReadName(),mastCellDegranulate.ReadValueWithProfile(INFLUENZASTRAIN,IGG));
    printf("%s.%s.e: %g\n",organName,mastCellDegranulate.ReadName(),mastCellDegranulate.ReadValueWithProfile(INFLUENZASTRAIN,IGE));
#endif                                 
    printf("%s.%s: %g\n",organName,tcEffector.ReadName(),tcEffector.ReadTotal());
    printf("%s.%s: %g\n",organName,igaBal.ReadName(),igaBal.ReadTotal());
    printf("%s.%s: %g\n",organName,antigenBal.ReadName(),antigenBal.ReadTotal());
    printf("%s.%s: %g\n",organName,bCellCentroblast.ReadName(),bCellCentroblast.ReadTotal());
    printf("%s.%s: %g\n",organName,bCellPlasmaMedullary.ReadName(),bCellPlasmaMedullary.ReadTotal());
    printf("%s.%s: %g\n",organName,tcBlast.ReadName(),tcBlast.ReadTotal());
    printf("%s.%s: %g\n",organName,thBlast.ReadName(),thBlast.ReadTotal());
    printf("%s.%s: %g\n",organName,macrophageApc.ReadName(),macrophageApc.ReadTotal());
    printf("%s.%s: %g\n",organName,dendriticApc.ReadName(),dendriticApc.ReadTotal());
  dendriticApc.Snapshot();
    printf("%s.%s: %g\n",organName,antigen.ReadName(),antigen.ReadTotal());
    printf("%s.%s: %g\n",organName,immuneComplex.ReadName(),immuneComplex.ReadTotal());
    printf("%s.epitheliaResistive: %g\n",organName,epitheliaResistive);
    printf("%s.epitheliaApc: %g\n",organName,epitheliaApc      );
    printf("%s.epitheliaDead: %g\n",organName,epitheliaDead      );
    printf("%s.epitheliaCell: %g\n",organName,epitheliaCell     );
    printf("%s.macrophage: %g\n",organName,macrophage        );
    printf("%s.dendriticImmature: %g\n",organName,dendriticImmature );

    printf("%s.%s: %g\n",organName,fdcApc.ReadName(),fdcApc.ReadTotal());
    printf("%s.%s: %g\n",organName,thGerminalCenter.ReadName(),thGerminalCenter.ReadTotal());
    printf("%s.%s: %g\n",organName,bCellCentrocyteApc.ReadName(),bCellCentrocyteApc.ReadTotal());
    printf("%s.%s: %g\n",organName,bCellCentrocyte.ReadName(),bCellCentrocyte.ReadTotal());
    printf("%s.%s: %g\n",organName,bCellCentrocyteInitial.ReadName(),bCellCentrocyteInitial.ReadTotal());
    printf("%s.%s: %g\n",organName,virtualThEffector.ReadName(),virtualThEffector.ReadTotal());
    printf("%s.%s: %g\n",organName,bCellBlast.ReadName(),bCellBlast.ReadTotal());
    printf("%s.%s: %g\n",organName,bCellApc.ReadName(),bCellApc.ReadTotal());
    printf("%s.%s: %g\n",organName,bCellNaiveRecirculate.ReadName(),bCellNaiveRecirculate.ReadValue(INFLUENZASTRAIN));
    printf("%s.%s: %g\n",organName,bCellNaive.ReadName(),bCellNaive.ReadValue(INFLUENZASTRAIN));
                                                  
    printf("%s.%s: %g\n",organName,bCellMemory.ReadName(),bCellMemory.ReadTotal());
    printf("%s.%s: %g\n",organName,bCellMemoryMarginal.ReadName(),bCellMemoryMarginal.ReadTotal());
    printf("%s.%s: %g\n",organName,thMemory.ReadName(),thMemory.ReadTotal());
    printf("%s.%s: %g\n",organName,tcMemory.ReadName(),tcMemory.ReadTotal());
    printf("%s.tcTotal: %g\n",organName, tcMemory.ReadTotal() + tcEffector.ReadTotal() );
       
    printf("%s.interferonAlpha: %g\n",organName,interferonAlpha / ( epitheliumvolume/ 1000.0)   );
    printf("%s.inflammatoryRate: %g\n",organName,inflammatoryRate);
    printf("%s.inflammatoryOutputRate: %g\n",organName,inflammatoryOutputRate);
    printf("%s.tnfAlpha: %g\n",organName,tnfAlpha/( epitheliumvolume/ 1000.0) );
    printf("%s.fdcGerminalCenter: %g\n",organName,fdcGerminalCenters);
    printf("%s.il2: %g\n",organName,il2/(tZoneVolume / 1000.0) );
    printf("%s.numberOfGerminalCenters: %g\n",organName,numberOfGerminalCenters );
                                     
                                                 
    printf("%s.%s: %g\n",organName,igM.ReadName(),igM.ReadTotal());
    rate = k2thPrecursorCount * il2 / (kmthPrecursorCount + il2);
    printf("%s.thPrecursorCount: %g\n",organName, 1.0 / (2.0 * 3600.0 * rate));
    rate = k2TcPrecursorCount * il2 / (kmTcPrecursorCount + il2);
    printf("%s.tcPrecursorCount: %g\n",organName, 1.0 / (2.0 * 3600.0 * rate));
                                                    
    return ;
#endif

    printFlag = 1;
 snapFlag = 1;
    bCellNaive.PrintValues(snapFlag);
    bCellNaiveRecirculate.PrintValues(snapFlag);
    bCellNaiveMarginalZone.PrintValues(snapFlag);
    bCellApc.PrintValues(snapFlag);
    bCellBlast.PrintValues(snapFlag);
    virtualThEffector.PrintValues(snapFlag);
    bCellCentroblast.PrintValues(snapFlag);
    bCellCentrocyteInitial.PrintValues(snapFlag);
    bCellCentrocyte.PrintValues(snapFlag);
    bCellCentrocyteApc.PrintValues(snapFlag);
    thGerminalCenter.PrintValues(snapFlag);
    fdcApc.PrintValues(snapFlag);
    plasmaCell.PrintValues(snapFlag);
    igaBal.PrintValues(snapFlag);
    bCellPlasmaMedullary.PrintValues(snapFlag);

    tcEffector.PrintValues(snapFlag);
    thEffector.PrintValues(snapFlag);
    dendriticApc.PrintValues(snapFlag);
    macrophageApc.PrintValues(snapFlag);
    antigenBal.PrintValues(snapFlag);

    for (i = 0; i < NUMBEROFBCENTROBLASTPRECURSOR; i++) {                                
        bCentroblastPrecursor[i].PrintValues(snapFlag);
    } /* iForLoop */                                        
    for (i = 0; i < NUMBEROFBPLASMAPRECURSOR; i++) {                                
        bPlasmaPrecursor[i].PrintValues(snapFlag);
    } /* iForLoop */                                        

    printf("%s:il2                :%g  (%g umole/ml) (tZoneVolume:%g ml)\n",organName,il2, il2/(tZoneVolume / 1000.0), (tZoneVolume / 1000.0)   );
    printf("%s:fdcGerminalCenter  :%g\n",organName,fdcGerminalCenters               );

 return;
#if 0

                

    printf("%s:macrophage         :%g\n",organName,macrophage        );
    printf("%s:dendriticImmature  :%g\n",organName,dendriticImmature );
    printf("%s:interferonAlpha    :%g\n",organName,interferonAlpha   );
    printf("%s:epitheliaResistive :%g\n",organName,epitheliaResistive);
    printf("%s:epitheliaApc       :%g\n",organName,epitheliaApc      );
    printf("%s:epitheliaDead       :%g\n",organName,epitheliaDead      );
    printf("%s:epitheliaCell      :%g\n",organName,epitheliaCell     );
    thNaive.PrintValues(snapFlag);
    tcNaive.PrintValues(snapFlag);

    thBlast.PrintValues(snapFlag);
    for (i = 0; i < NUMBEROFTHBLASTPRECURSOR; i++) {
        thBlastPrecursor[i].PrintValues(snapFlag);
    } /* iForLoop */
    for (i = 0; i < NUMBEROFTHEFFECTORPRECURSOR; i++) {
        thEffectorPrecursor[i].PrintValues(snapFlag);
    } /* iForLoop */

    tcBlast.PrintValues(snapFlag);
    for (i = 0; i < NUMBEROFTCBLASTPRECURSOR; i++) {
        tcBlastPrecursor[i].PrintValues(snapFlag);
    } /* iForLoop */
    for (i = 0; i < NUMBEROFTCEFFECTORPRECURSOR; i++) {
        tcEffectorPrecursor[i].PrintValues(snapFlag);
    } /* iForLoop */
#endif
}



void  GenericImmuneTissue::ExecuteLymphJunction ()
{
    // printf("bloodbCellNaiveRecirculate: rate:%g  (k2:%g)\n",lymphOutputbCellNaiveRecirculate[0] * k2LymphJunction, k2LymphJunction);
    lymphOutputbCellNaiveRecirculate.MigrateOutput( bloodbCellNaiveRecirculate ,k2LymphJunction) ;
    lymphOutputThNaive.MigrateOutput( bloodThNaive ,k2LymphJunction) ;
    lymphOutputTcNaive.MigrateOutput( bloodTcNaive ,k2LymphJunction) ;
    lymphOutputtcEffector.MigrateOutput( bloodtcEffector ,k2LymphJunction) ;
    lymphOutputthEffector.MigrateOutputWithProfile( bloodthEffector ,k2LymphJunction) ;
    lymphOutputplasmaCell.MigrateOutputWithProfile( bloodplasmaCell ,k2LymphJunction) ;
    lymphOutputigM.MigrateOutput( bloodigM ,k2LymphJunction) ;
    lymphOutputbCellMemory.MigrateOutputWithProfile( bloodbCellMemory ,k2LymphJunction) ;
    lymphOutputthMemory.MigrateOutputWithProfile( bloodthMemory ,k2LymphJunction) ;
    lymphOutputtcMemory.MigrateOutputWithProfile( bloodtcMemory ,k2LymphJunction) ;
}



void  GenericImmuneTissue::ExecuteBoneMarrow ()
{
    double  rate;
    int  i;
    rate = kHalfLifeGmcsf * bloodgmcsf ;
    bloodgmcsf -= rate;
    rate = kHalfLifeil3 * bloodil3 ;
    bloodil3 -= rate;
    rate = kHalfLifeil5 * bloodil5 ;
    bloodil5 -= rate;
                 
    bloodeosinophil += kGenerateeosinophil * (1.0 + knGenerateeosinophil * bloodil5 / (kmGenerateeosinophil + bloodil5));
    bloodmastCell += kGeneratemastCell * (1.0 + knGeneratemastCell * bloodil3 / (kmGeneratemastCell + bloodil3));
    bloodmonocyte += kGenerateMonocyte * (1.0 + knGenerateMonocyte * bloodgmcsf / (kmGenerateMonocyte + bloodgmcsf));
    bloodplatelets += kGeneratePlatelets;
    bloodrbc += kGenerateRbc;
    bloodbCellNaive.AddStrain(BACKGROUNDSTRAIN, kGenerateBCells);
    bloodThNaive.AddStrain(BACKGROUNDSTRAIN , kGenerateThCells);
    bloodTcNaive.AddStrain(BACKGROUNDSTRAIN , kGenerateTcCells);
    for (i = BACKGROUNDSTRAIN + 1; i < TOTALSTRAINS; i++) {
        bloodbCellNaive.AddStrain(i, kGenerateBCells * STRAINFREQUENCY);
        bloodThNaive.AddStrain(i , kGenerateThCells * STRAINFREQUENCY);
        bloodTcNaive.AddStrain(i , kGenerateTcCells * STRAINFREQUENCY);
    } /* iForLoop */     

    bloodthEffector.MigrateOutput(thEffector , k2BloodInput_thEffector) ;
    bloodtcEffector.MigrateOutput(tcEffector , k2BloodInput_tcEffector) ;
    bloodplasmaCell.MigrateOutputWithProfile(plasmaCell, k2BloodInputPlasmaCell) ;
    plasmaCell.MigrateOutput(kHalfLifePlasmaCell);
    tcEffector.MigrateAicd(dendriticApc, k2tcAicd,kmtcAicd,k0tcAicd); 
    thEffector.MigrateAicd(dendriticApc, k2thAicd,kmthAicd,k0thAicd); 
    tcEffector.ApcDeActivate(bloodtcMemory,dendriticApc, k2TcEffector2Memory,kmTcEffector2Memory);
    thEffector.ApcDeActivate(bloodthMemory,dendriticApc, k2ThEffector2Memory,kmThEffector2Memory);
}

                                                  
int  GenericImmuneTissue::FindTissueIndex (char *s)
{
    int  i ;
    for (i = 0; i < NUMBEROFTISSUECONSTANTS; i++) {
        if (strcmp(s, tissueConstants[i].name) == 0) {
            return(i) ;
        } /* if */
    } /* iForLoop */
    printf("FindTissueIndex: can't find: %s\n",s);
    exit(1) ;
    return(0) ;
}




void  GenericImmuneTissue::ExecuteIntestines ()
{
    ExecuteGeneralTissue();
}


void  GenericImmuneTissue::ExecuteLungs ()
{
    ExecuteGeneralTissue();
}




void  GenericImmuneTissue::ExecuteLiver ()
{
    double  rate;

    rate = bloodplatelets * k2BloodInput_platelets;
    bloodplatelets -= rate ;

    ExecuteGeneralTissue();
}

                           
void  GenericImmuneTissue::ExecuteGeneralTissue ()
{
    double  rate;

    bCellMemory.MigrateOutputWithProfile(lymphOutputbCellMemory , k2LymphOutput_bCellMemory) ;
    thMemory.MigrateOutputWithProfile(lymphOutputthMemory , k2LymphOutput_thMemory) ;
    tcMemory.MigrateOutputWithProfile(lymphOutputtcMemory , k2LymphOutput_tcMemory) ;
    bloodbCellMemory.MigrateOutputWithProfile(bCellMemory , k2BloodInput_bCellMemory) ;
    bloodthMemory.MigrateOutputWithProfile( thMemory, k2BloodInput_thMemory) ;
    bloodtcMemory.MigrateOutputWithProfile( tcMemory, k2BloodInput_tcMemory) ;

    bloodbCellNaiveRecirculate.MigrateOutput(bCellNaiveRecirculate , k2BloodInput_bCellNaiveRecirculate) ;
    bloodthEffector.MigrateOutputWithProfile(thEffector , k2BloodInput_thEffector) ;
    bloodtcEffector.MigrateOutput(tcEffector , k2BloodInput_tcEffector) ;
    bloodplasmaCell.MigrateOutputWithProfile(plasmaCell, k2BloodInputPlasmaCell) ;

    bCellNaiveRecirculate.MigrateOutput(lymphOutputbCellNaiveRecirculate , k2LymphOutput_bCellNaiveRecirculate) ;

    rate = bloodmonocyte * k2BloodInput_Macrophage;
    bloodmonocyte -= rate ;
    macrophage += rate;

    rate = bloodmastCell * k2BloodInput_mastCell;
    bloodmastCell -= rate ;
    mastCellNaive += rate;

    rate = bloodeosinophil * k2BloodInput_eosinophil ;
    bloodeosinophil -= rate ;
    eosinophil += rate;

    rate = bloodmonocyte * k2BloodInput_Dendritic;
    bloodmonocyte -= rate ;
    dendriticImmature += rate;

    /* die stuff (for now) */
    rate = macrophage * (k2MacrophageDie - k2macrophageReplicate);
    macrophage -= rate;     
    
    rate = (k2DendriticDie - k2DendriticReplicate) * dendriticImmature;
    dendriticImmature -= rate;

    plasmaCell.MigrateOutput(kHalfLifePlasmaCell);

    tcEffector.MigrateAicd(dendriticApc, k2tcAicd,kmtcAicd,k0tcAicd); 
    thEffector.MigrateAicd(dendriticApc, k2thAicd,kmthAicd,k0thAicd); 
    tcEffector.ApcDeActivate(tcMemory,dendriticApc, k2TcEffector2Memory,kmTcEffector2Memory);
    thEffector.ApcDeActivate(thMemory,dendriticApc, k2ThEffector2Memory,kmThEffector2Memory);
}
                             
                           
void  GenericImmuneTissue::ExecuteLymphNodeGeneral ()
{

    bCellMemory.MigrateOutputWithProfile(lymphOutputbCellMemory , k2LymphOutput_bCellMemory) ;
    thMemory.MigrateOutputWithProfile(lymphOutputthMemory , k2LymphOutput_thMemory) ;
    tcMemory.MigrateOutputWithProfile(lymphOutputtcMemory , k2LymphOutput_tcMemory) ;

    lymphInputbCellMemory.MigrateOutputWithProfile(bCellMemory  , k2LymphInput_bCellMemory) ;
    lymphInputthMemory.MigrateOutputWithProfile( thMemory , k2LymphInput_thMemory) ;
    lymphInputtcMemory.MigrateOutputWithProfile( tcMemory , k2LymphInput_tcMemory) ;

    lymphInputbCellNaiveRecirculate.MigrateOutput(bCellNaiveRecirculate , k2LymphInput_bCellNaiveRecirculate) ;

    bCellNaiveRecirculate.MigrateOutput(lymphOutputbCellNaiveRecirculate , k2LymphOutput_bCellNaiveRecirculate) ;
    thNaive.MigrateOutput(lymphOutputThNaive , k2LymphOutput_thNaive) ;
    tcNaive.MigrateOutput(lymphOutputTcNaive , k2LymphOutput_tcNaive) ;

    bloodTcNaive.MigrateOutput(tcNaive , k2BloodInput_tcNaive) ;
    tcNaive.MigrateOutput( k2tcNaiveDie) ;
    bloodThNaive.MigrateOutput(thNaive , k2BloodInput_thNaive) ;
    thNaive.MigrateOutput( k2thNaiveDie) ;

    bloodbCellNaive.MigrateOutput(bCellNaive , k2BloodInput_bCellNaive) ;
    bloodbCellNaiveRecirculate.MigrateOutput(bCellNaiveRecirculate , k2BloodInput_bCellNaiveRecirculate) ;
    bCellNaive.MigrateOutput( k2bCellNaiveDie) ;
    bCellNaive.MigrateOutput( bCellNaiveRecirculate ,k2bCellNaiveFollicle / (kibCellNaiveFollicle + bCellNaiveRecirculate.ReadTotal()) ) ;
    bCellNaiveRecirculate.MigrateOutput(k2bCellRecirculateDie * bCellNaive.ReadTotal() ) ;
}
                           
  
void  GenericImmuneTissue::ExecutePeyersPatch ()
{

    bCellMemory.MigrateOutputWithProfile(lymphOutputbCellMemory , k2LymphOutput_bCellMemory) ;
    thMemory.MigrateOutputWithProfile(lymphOutputthMemory , k2LymphOutput_thMemory) ;
    tcMemory.MigrateOutputWithProfile(lymphOutputtcMemory , k2LymphOutput_tcMemory) ;


    ExecuteLymphNodeInternal ();
 /* test!!! */ 
 bCellCentrocyte.MigrateOutputWithProfile(lymphOutputbCellMemory,k2Centrocyte2bCellMemory);
                                        
    bCellNaiveRecirculate.MigrateOutput(lymphOutputbCellNaiveRecirculate , k2LymphOutput_bCellNaiveRecirculate) ;
    thNaive.MigrateOutput(lymphOutputThNaive , k2LymphOutput_thNaive) ;
    tcNaive.MigrateOutput(lymphOutputTcNaive , k2LymphOutput_tcNaive) ;
    tcEffector.MigrateOutput(lymphOutputtcEffector , k2LymphOutput_tcEffector) ;
    thEffector.MigrateOutputWithProfile(lymphOutputthEffector , k2LymphOutput_thEffector) ;
    plasmaCell.MigrateOutputWithProfile(lymphOutputplasmaCell, k2LymphOutput_plasmaCell);
    igM.MigrateOutput(lymphOutputigM , k2LymphOutput_igM) ;
}
  

void  GenericImmuneTissue::ExecuteLymphNode ()
{
                            
    bCellMemory.MigrateOutputWithProfile(lymphOutputbCellMemory , k2LymphOutput_bCellMemory) ;
    thMemory.MigrateOutputWithProfile(lymphOutputthMemory , k2LymphOutput_thMemory) ;
    tcMemory.MigrateOutputWithProfile(lymphOutputtcMemory , k2LymphOutput_tcMemory) ;

    lymphInputbCellMemory.MigrateOutputWithProfile(bCellMemory  , k2LymphInput_bCellMemory) ;
    lymphInputthMemory.MigrateOutputWithProfile( thMemory , k2LymphInput_thMemory) ;
    lymphInputtcMemory.MigrateOutputWithProfile( tcMemory , k2LymphInput_tcMemory) ;

    lymphInputbCellNaiveRecirculate.MigrateOutput(bCellNaiveRecirculate , k2LymphInput_bCellNaiveRecirculate) ;
    lymphInputmacrophageApc.MigrateOutput(macrophageApc  , k2LymphInput_macrophageApc) ;
    lymphInputdendriticApc.MigrateOutputWithProfile(dendriticApc  , k2LymphInput_dendriticApc) ;

    ExecuteLymphNodeInternal ();
 /* test!!! */ 
 bCellCentrocyte.MigrateOutputWithProfile(lymphOutputbCellMemory,k2Centrocyte2bCellMemory);
                                        
    bCellNaiveRecirculate.MigrateOutput(lymphOutputbCellNaiveRecirculate , k2LymphOutput_bCellNaiveRecirculate) ;
    thNaive.MigrateOutput(lymphOutputThNaive , k2LymphOutput_thNaive) ;
    tcNaive.MigrateOutput(lymphOutputTcNaive , k2LymphOutput_tcNaive) ;
    tcEffector.MigrateOutput(lymphOutputtcEffector , k2LymphOutput_tcEffector) ;
    thEffector.MigrateOutputWithProfile(lymphOutputthEffector , k2LymphOutput_thEffector) ;
    plasmaCell.MigrateOutputWithProfile(lymphOutputplasmaCell, k2LymphOutput_plasmaCell);
    igM.MigrateOutput(lymphOutputigM , k2LymphOutput_igM) ;
}
  

void  GenericImmuneTissue::ExecuteSpleen ()
{                      
    double  rate;

    bloodbCellMemory.MigrateOutputWithProfile(bCellMemory , k2BloodInput_bCellMemory) ;
    bloodthMemory.MigrateOutputWithProfile( thMemory, k2BloodInput_thMemory) ;
    bloodtcMemory.MigrateOutputWithProfile( tcMemory, k2BloodInput_tcMemory) ;

    bCellMemory.MigrateOutputWithProfile( bloodbCellMemory, k2BloodOutput_bCellMemory) ;
    thMemory.MigrateOutputWithProfile( bloodthMemory, k2BloodOutput_thMemory) ;
    tcMemory.MigrateOutputWithProfile( bloodtcMemory, k2BloodOutput_tcMemory) ;

    bCellNaive.MigrateOutput( bloodbCellNaive, k2BloodOutput_bCellNaive) ;
    bCellNaiveRecirculate.MigrateOutput( bloodbCellNaiveRecirculate, k2BloodOutput_bCellNaiveRecirculate) ;
    // GenericImmuneCell::ResetPrint(printFlag);
    thNaive.MigrateOutput( bloodThNaive, k2BloodOutput_thNaive);
    tcNaive.MigrateOutput( bloodTcNaive, k2BloodOutput_tcNaive);
    // printFlag = 0;
    // GenericImmuneCell::ResetPrint(printFlag);

    bCellNaiveRecirculate.MigrateOutput( bCellNaiveMarginalZone ,k2bCellNaiveFollicle / (kibCellNaiveFollicle + bCellNaiveMarginalZone.ReadTotal()) ) ;
    bCellNaiveMarginalZone.MigrateOutput(k2bCellRecirculateDie * bCellNaive.ReadTotal() ) ;

    rate = bloodrbc * k2BloodInput_rbc;
    bloodrbc -= rate ;
    rate = bloodplatelets * k2BloodInput_platelets;
    bloodplatelets -= rate ;

    rate = bloodmonocyte * k2BloodInput_Macrophage;
    bloodmonocyte -= rate ;
    macrophage += rate;

    /* die stuff (for now) */
    rate = macrophage * (k2MacrophageDie - k2macrophageReplicate);
    macrophage -= rate;
}
                                                    



void  GenericImmuneTissue::ExecuteLymphNodeInternal ()
{
    double  rate; 
    int  i;

    dendriticApc.MigrateOutput(kHalfLifeDendriticApc);
    rate = kHalfLifeIl2 * il2 ;
    il2 -= rate ;

    /* Tc cell */                    
    bloodTcNaive.MigrateOutput(tcNaive , k2BloodInput_tcNaive) ;
    tcNaive.MigrateOutput( k2tcNaiveDie) ;
    tcNaive.ApcActivate(tcBlastPrecursor[0],dendriticApc,k2TcNaiveActivate,kmTcNaiveActivate);

    rate = k2BlastIl2 * tcBlastPrecursorTotal;
    il2 += rate;

    tcBlastCount += tcBlastDCount ;
    if (tcBlastCount >= 1.0) {
        printf("*********************** tcBlastCount\n");
        tcBlastCount = 0.0;
        tcBlastPrecursor[3].ActivatePrecursor(tcBlast,dendriticApc,tcAnergy, k2TcBlastPrecursorActivate,kmTcBlastPrecursorActivate);
        tcBlastPrecursor[2].ActivatePrecursor(tcBlastPrecursor[3],dendriticApc,tcAnergy, k2TcBlastPrecursorActivate,kmTcBlastPrecursorActivate);
        tcBlastPrecursor[1].ActivatePrecursor(tcBlastPrecursor[2],dendriticApc,tcAnergy, k2TcBlastPrecursorActivate,kmTcBlastPrecursorActivate);
        tcBlastPrecursor[0].ActivatePrecursor(tcBlastPrecursor[1],dendriticApc,tcAnergy, k2TcBlastPrecursorActivate,kmTcBlastPrecursorActivate);

        tcBlastPrecursorTotal = tcBlastPrecursor[1].ReadTotal() + tcBlastPrecursor[2].ReadTotal() + tcBlastPrecursor[3].ReadTotal() + tcBlast.ReadTotal();
    } /* if */
                                                    
    rate = k2TcPrecursorCount * il2 / (kmTcPrecursorCount + il2);
    tcPrecursorCount += rate ;
    if (tcPrecursorCount >= 1.0) {
        printf("####################### shifting: rate:%g hours, il2:%g\n",1.0 / (2.0 * 3600.0 * rate),il2);
        tcPrecursorCount = 0.0 ;
        tcEffectorPrecursor[NUMBEROFTCEFFECTORPRECURSOR - 1].Replicate(tcEffector,kTcBlastReplicate,2.0) ;
        for (i = (NUMBEROFTCEFFECTORPRECURSOR - 2); i >= 0; i--) {
            tcEffectorPrecursor[i].Replicate(tcEffectorPrecursor[i + 1],kTcBlastReplicate,2.0);
        } /* iForLoop */
        tcBlast.Replicate(tcEffectorPrecursor[0],kTcBlastReplicate,2.0) ;
        for (i = 0, adjustTcBlast = 0.0; i < NUMBEROFTCEFFECTORPRECURSOR; i++) {
            if (i < TCEFFECTORCUTOFF) {
                adjustTcBlast += tcEffectorPrecursor[i].ReadTotal(); /* blast transitions to effector */ 
            } /* if */     
        } /* iForLoop */
    } /* if */        

    tcMemory.ApcActivate(tcBlastMemory,dendriticApc,k2TcMemoryActivate,kmTcMemoryActivate);
    rate = k2TcPrecursorCountMemory * il2 / (kmTcPrecursorCountMemory + il2);
    tcPrecursorCountMemory += rate ;
    if (tcPrecursorCountMemory >= 1.0) {
        tcPrecursorCountMemory = 0.0 ;
        tcEffectorPrecursorMemory[NUMBEROFTCEFFECTORPRECURSORMEMORY - 1].Replicate(tcEffector,kTcBlastReplicateMemory,2.0) ;
        for (i = (NUMBEROFTCEFFECTORPRECURSORMEMORY - 2); i >= 0; i--) {
            tcEffectorPrecursorMemory[i].Replicate(tcEffectorPrecursorMemory[i + 1],kTcBlastReplicateMemory,2.0);
        } /* iForLoop */                                                                                   
        tcBlastMemory.Replicate(tcEffectorPrecursorMemory[0],kTcBlastReplicateMemory,2.0) ;
        for (i = 0, adjustTcBlastMemory = 0.0 ; i < NUMBEROFTCEFFECTORPRECURSORMEMORY; i++) {
            if (i < TCEFFECTORCUTOFFMEMORY) {
                adjustTcBlastMemory += tcEffectorPrecursorMemory[i].ReadTotal(); /* blast transitions to effector */ 
            } /* if */     
        } /* iForLoop */
    } /* if */        

    rate = k2EffectorPrecursorIl2 * (adjustTcBlast + adjustTcBlastMemory) ;
    il2 += rate ;
    rate = k2EffectorPrecursorIl2Autocrine * (adjustTcBlast + adjustTcBlastMemory) * il2 ;
    il2 -= rate ;            

                  
    /* Th cell */                    
    bloodThNaive.MigrateOutput(thNaive , k2BloodInput_thNaive) ;
    thNaive.MigrateOutput( k2thNaiveDie) ;
    thNaive.ApcActivate(thBlastPrecursor[0],dendriticApc,k2ThNaiveActivate,kmThNaiveActivate);

    rate = k2BlastIl2 * thBlastPrecursorTotal;
    il2 += rate;
 
    thBlastCount += thBlastDCount ;   
    if (thBlastCount >= 1.0) {
        thBlastCount = 0.0;    
        thBlastPrecursor[3].ActivatePrecursor(thBlast,dendriticApc,thAnergy, k2thBlastPrecursorActivate,kmthBlastPrecursorActivate);
        thBlastPrecursor[2].ActivatePrecursor(thBlastPrecursor[3],dendriticApc,thAnergy, k2thBlastPrecursorActivate,kmthBlastPrecursorActivate);
        thBlastPrecursor[1].ActivatePrecursor(thBlastPrecursor[2],dendriticApc,thAnergy, k2thBlastPrecursorActivate,kmthBlastPrecursorActivate);
        thBlastPrecursor[0].ActivatePrecursor(thBlastPrecursor[1],dendriticApc,thAnergy, k2thBlastPrecursorActivate,kmthBlastPrecursorActivate);

        thBlastPrecursorTotal = thBlastPrecursor[2].ReadTotal() + thBlastPrecursor[3].ReadTotal() + thBlast.ReadTotal();
    } /* if */                        

    rate = k2thPrecursorCount * il2 / (kmthPrecursorCount + il2);
    thPrecursorCount += rate ;
    if (thPrecursorCount >= 1.0) {
        thPrecursorCount = 0.0 ;
        thEffectorPrecursor[NUMBEROFTHEFFECTORPRECURSOR - 1].Replicate(thEffector,kthBlastReplicate,2.0) ;
        for (i = (NUMBEROFTHEFFECTORPRECURSOR - 2); i >= 0; i--) {
            thEffectorPrecursor[i].Replicate(thEffectorPrecursor[i + 1],kthBlastReplicate,2.0);
        } /* iForLoop */
        thBlast.Replicate(thEffectorPrecursor[0],kthBlastReplicate,2.0) ;

        virtualThEffector.ClearValues();
        for (i = 0; i < NUMBEROFTHEFFECTORPRECURSOR; i++) {
            thEffectorPrecursor[i].Polarization(dendriticApc,  k2PolarizationTh1, kmPolarizationTh1, k2PolarizationTh2, kmPolarizationTh2 );
            thEffectorPrecursor[i].CopyOutputWithProfile(virtualThEffector,1.0);
        } /* iForLoop */     
        thEffector.CopyOutputWithProfile(virtualThEffector,1.0);
        thEffectorPrecursorTotal = virtualThEffector.ReadTotal();
        th2EffectorPrecursorTotal = virtualThEffector.ReadTotal(TH2);
    } /* if */              

    thMemory.ApcActivate(thBlastMemory,dendriticApc,k2ThMemoryActivate,kmThMemoryActivate);
    rate = k2thPrecursorCountMemory * il2 / (kmthPrecursorCountMemory + il2);
    thPrecursorCountMemory += rate ;
    if (thPrecursorCountMemory >= 1.0) {
        thPrecursorCountMemory = 0.0 ;
        thEffectorPrecursorMemory[NUMBEROFTHEFFECTORPRECURSORMEMORY - 1].Replicate(thEffector,kthBlastReplicateMemory,2.0) ;
        for (i = (NUMBEROFTHEFFECTORPRECURSORMEMORY - 2); i >= 0; i--) {
            thEffectorPrecursorMemory[i].Replicate(thEffectorPrecursorMemory[i + 1],kthBlastReplicateMemory,2.0);
        } /* iForLoop */
        thBlastMemory.Replicate(thEffectorPrecursorMemory[0],kthBlastReplicateMemory,2.0) ;
                                     
        virtualThEffectorMemory.ClearValues();
        thEffectorPrecursorMemory[0].RePolarization(dendriticApc,  k2PolarizationTh1, kmPolarizationTh1, k2PolarizationTh2, kmPolarizationTh2 );
        for (i = 1; i < NUMBEROFTHEFFECTORPRECURSOR; i++) {
            thEffectorPrecursorMemory[i].Polarization(dendriticApc,  k2PolarizationTh1, kmPolarizationTh1, k2PolarizationTh2, kmPolarizationTh2 );
            thEffectorPrecursorMemory[i].CopyOutputWithProfile(virtualThEffectorMemory,1.0);
        } /* iForLoop */     
        thEffectorPrecursorTotalMemory = virtualThEffectorMemory.ReadTotal();
        th2EffectorPrecursorTotalMemory = virtualThEffectorMemory.ReadTotal(TH2);
    } /* if */                   

    rate = k2EffectorPrecursorIl2 * (thEffectorPrecursorTotal + thEffectorPrecursorTotalMemory - th2EffectorPrecursorTotal - th2EffectorPrecursorTotalMemory );
    il2 += rate ;
    rate = k2EffectorPrecursorIl2Autocrine * (thEffectorPrecursorTotal + thEffectorPrecursorTotalMemory) * il2 ;
    il2 -= rate ;            


    /* bCell */ 
    bloodbCellNaive.MigrateOutput(bCellNaive , k2BloodInput_bCellNaive) ;
    bloodbCellNaiveRecirculate.MigrateOutput(bCellNaiveRecirculate , k2BloodInput_bCellNaiveRecirculate) ;
    bCellNaive.MigrateOutput( k2bCellNaiveDie) ;
    bCellNaive.MigrateOutput( bCellNaiveRecirculate ,k2bCellNaiveFollicle / (kibCellNaiveFollicle + bCellNaiveRecirculate.ReadTotal()) ) ;
    bCellNaiveRecirculate.MigrateOutput(k2bCellRecirculateDie * bCellNaive.ReadTotal() ) ;

    bCellNaiveRecirculate.ApcActivate(bCellApc,dendriticApc,k2bCellNaiveRecirculateActivate,kmbCellNaiveRecirculateActivate);
    bCellNaive.ApcActivate(bCellApc,dendriticApc,k2bCellNaiveRecirculateActivate,kmbCellNaiveRecirculateActivate);
    bCellApc.MigrateOutput(kHalfLifebCellApc);
    bCellApc.ApcActivate(bCellBlast,virtualThEffector,k2bCellApcActivate,kmbCellApcActivate);

    bCellMemoryMarginal.ApcActivate(bCellApcMemory,antigen,k2bCellMemoryMarginalActivate,kmbCellMemoryMarginalActivate);
    bCellMemory.ApcActivate(bCellApcMemory,dendriticApc,k2bCellMemoryActivate,kmbCellMemoryActivate);
    bCellApcMemory.MigrateOutput(kHalfLifebCellApcMemory);
    bCellApcMemory.ApcActivate(bCellBlastMemory,virtualThEffector,k2bCellApcMemoryActivate,kmbCellApcMemoryActivate);
                                      
    bBlastCount += bBlastDCount ;   
    if (bBlastCount >= 1.0) {
        bBlastCount = 0.0;
        bCentroblastPrecursor[NUMBEROFBCENTROBLASTPRECURSOR - 1].Replicate(bCellCentroblast,kbCentroblastReplicate,2.0) ;
        for (i = (NUMBEROFBCENTROBLASTPRECURSOR - 2); i >= 0; i--) {
            bCentroblastPrecursor[i].Replicate(bCentroblastPrecursor[i + 1],kbCentroblastReplicate,2.0);
        } /* iForLoop */
        bCellBlast.Replicate(bCentroblastPrecursor[0],kbCentroblastReplicateInitial,2.0) ;
        bCellBlastMemory.Replicate(bCentroblastPrecursor[0],kbCentroblastReplicateInitialMemory,2.0) ;
        for (i = 0; i < NUMBEROFBCENTROBLASTPRECURSOR; i++) {
            bCentroblastPrecursor[i].ClassSwitches (virtualThEffector,dendriticApc,  k2SwitchesIgg, kmSwitchesIgg, k2SwitchesIga, kmSwitchesIga, kiSwitchesIga ,k2SwitchesIgg1, kmSwitchesIgg1, k2SwitchesIge, kmSwitchesIge);
        } /* iForLoop */     
        printf("number of germinal centers: %g\n",numberOfGerminalCenters);
    } /* if */                        
    numberOfGerminalCenters = bCellCentroblast.ReadTotal() / CENTROBLASTPERGERMINALCENTER ;
    if (numberOfGerminalCenters < 0.001) {
        numberOfGerminalCenters = 0.001;
    } /* if */     

    /* bCell germinal center */ 
    bCellCentroblast.MigrateOutput(bCellDeadCentroblast,kHalfLifebCellCentroblast);
    bCellCentroblast.CopyOutputWithProfile(bCellCentrocyteInitial,k2Centroblast2Centrocyte);
    bCellCentrocyteInitial.ApcActivateWithoutStrain(bCellCentrocyteApc,fdcApc,fdcGerminalCenters,k2bCellCentrocyteInitialActivate,kmbCellCentrocyteInitialActivate * numberOfGerminalCenters,knbCellCentrocyteInitialActivate);
    bCellCentrocyteApc.ApcActivate(bCellCentrocyte,thGerminalCenter,k2bCellCentrocyteActivate,kmbCellCentrocyteActivate * numberOfGerminalCenters);
    bCellCentrocyteInitial.MigrateOutput(kHalfLifebCellCentrocyteInitial);
    bCellCentrocyteApc.MigrateOutput(kHalfLifebCellCentrocyteApc);
    bCellCentrocyte.MigrateCentroblastWithProfile(bCellCentroblast,bCellDeadCentroblast, k2Centrocyte2Centroblast);
    bCellCentrocyte.MigrateOutputWithProfile(plasmaCell,k2Centrocyte2PlasmaCell);
//  bCellCentrocyte.MigrateOutputWithProfile(bCellMemory,k2Centrocyte2bCellMemory);
    bCellCentrocyte.MigrateOutputWithProfile(bCellMemoryMarginal,k2Centrocyte2bCellMemoryMarginal);

    rate = numberOfGerminalCenters * MAXIMUMTHPERGERMINALCENTER - thGerminalCenter.ReadTotal() ;
    if (rate > 0.0) {        
        thEffector.MigrateOutput(thGerminalCenter, k2Effector2GerminalCenter);
    } /* if */     
    thGerminalCenter.MigrateOutput(kHalfLifeThGerminalCenter) ;

    rate = numberOfGerminalCenters * MAXIMUMFDCPERGERMINALCENTER - fdcApc.ReadTotal() ;
    if (rate > 0.0) {        
        fdcApc.ApcActivateWithoutStrain(fdcGerminalCenters, immuneComplex,k2FdcApc, kmFdcApc, knFdcApc);
    } /* if */     
    
    
    /* red pulp */ 
    bPlasmaCount += bPlasmaDCount ;   
    if (bPlasmaCount >= 1.0) {
        bPlasmaCount = 0.0;
        bPlasmaPrecursor[NUMBEROFBPLASMAPRECURSOR - 1].ReplicateSpecial(bCellPlasmaMedullary,plasmaCell,kbPlasmaReplicate,kbPlasmaReplicateDecision) ;
        for (i = (NUMBEROFBPLASMAPRECURSOR - 2); i >= 0; i--) {
            bPlasmaPrecursor[i].Replicate(bPlasmaPrecursor[i + 1],kbPlasmaReplicate,2.0);
        } /* iForLoop */
        bCellBlast.Replicate(bPlasmaPrecursor[0],kbPlasmaReplicateInitial,2.0) ;
        bCellBlastMemory.Replicate(bPlasmaPrecursor[0],kbPlasmaReplicateInitialMemory,2.0) ;
    } /* if */                        
                                                  
    bCellPlasmaMedullary.CopyOutputExtractProfile(igM,k2PlasmaMedullary2IgM, IGM);
    bCellPlasmaMedullary.MigrateOutput(kHalfLifebCellPlasmaMedullary);

    antigen.MigrateOutputWithProfile(immuneComplex,igM,k2immuneComplex,knimmuneComplex);
    macrophageApc.Replicate(antigen,kHalfLifeMacrophageApc,knMacrophageApc); /* macrophageApc dies */ 
    
#if 1
    /* ?  Tests ?  */            
    rate = k2EffectorKill * macrophageApc.ReadValue(INFLUENZASTRAIN) * tcEffector.ReadValue(INFLUENZASTRAIN) ;  
    macrophageApc.AddStrain(INFLUENZASTRAIN,-rate) ;
    tcEffector.AddStrain(INFLUENZASTRAIN,-rate * knEffectorKill) ;
    rate = k2EffectorKillDendritic * dendriticApc.ReadValue(INFLUENZASTRAIN) * tcEffector.ReadValue(INFLUENZASTRAIN) ;  
    dendriticApc.AddStrain(INFLUENZASTRAIN,-rate) ;
    tcEffector.AddStrain(INFLUENZASTRAIN,-rate * knEffectorKill) ;
#endif    

}                           


                                     
void  GenericImmuneTissue::ExecuteInfusion (int  infusionFlag)
{
    if (infusionFlag) {
        // antigenBal.AddStrain(INFLUENZASTRAIN, 2.9e4 * 420.0);
         antigenBal.AddStrain(RYEGRASSSTRAIN, 1.2e8 );
#if 0
        macrophage = 0.0;
        dendriticImmature = 0.0;
        macrophage +=  2.3e10 * BRONCHIALFRACTION;
        dendriticImmature += 2.3e8 * BRONCHIALFRACTION;
#endif
    } /* if */     
#if 0                       
    igaBal.ClearValues();
    plasmaCell.ClearValues();
    bloodplasmaCell.ClearValues();
    // lymphInputplasmaCell.ClearValues();
    lymphOutputplasmaCell.ClearValues();
#endif
}

 

double  GenericImmuneTissue::stepTime = 0.0;
GenericImmuneTissue::GenericImmuneTissue(VesselSegment *newCapillary, VesselSegment *newInputLymphDuct, VesselSegment *newOutputLymphDuct, VesselSegment *newbloodReservoir,
  double  newWeight, double  newVolume, char *newModelName, char *newOrganName ,double  newdTime   ) :
    bloodmonocyte( newCapillary->FindSubstance("monocyte", '-')        ),
    bloodplatelets( newCapillary->FindSubstance("platelets", '-')        ),
    bloodrbc( newCapillary->FindSubstance("rbc", '-')        ),
    bloodgmcsf( newCapillary->FindSubstance("gmcsf", '-')        ),
    bloodil3( newCapillary->FindSubstance("il3", '-')        ),
    bloodil5( newCapillary->FindSubstance("il5", '-')        ),
    bloodeosinophil( newCapillary->FindSubstance("eosinophil", '-')        ),
    bloodmastCell( newCapillary->FindSubstance("mastCell", '-')        ),

    bloodbCellMemory      ( newbloodReservoir->FindImmuneCell(  "bCellMemory"                    )),
    bloodthMemory      ( newbloodReservoir->FindImmuneCell(     "thMemory"                    )),
    bloodtcMemory      ( newbloodReservoir->FindImmuneCell(     "tcMemory"                    )),
    lymphInputbCellMemory          ( newInputLymphDuct->FindImmuneCell(  "bCellMemory"   )),
    lymphInputthMemory             ( newInputLymphDuct->FindImmuneCell(  "thMemory"      )),
    lymphInputtcMemory             ( newInputLymphDuct->FindImmuneCell(  "tcMemory"      )),
    lymphOutputbCellMemory               ( newOutputLymphDuct->FindImmuneCell( "bCellMemory"      )),
    lymphOutputthMemory                  ( newOutputLymphDuct->FindImmuneCell( "thMemory"         )),
    lymphOutputtcMemory                  ( newOutputLymphDuct->FindImmuneCell( "tcMemory"         )),
    bloodtcEffector       ( newbloodReservoir->FindImmuneCell(     "tcEffector"                    )),
    bloodThNaive                     ( newbloodReservoir->FindImmuneCell(        "thNaive"                      )),
    bloodTcNaive                     ( newbloodReservoir->FindImmuneCell(        "tcNaive"                      )),
    bloodbCellNaive                  ( newbloodReservoir->FindImmuneCell(        "bCellNaive"                   )),
    bloodbCellNaiveRecirculate       ( newbloodReservoir->FindImmuneCell(        "bCellNaiveRecirculate"        )),
    lymphInputmacrophageApc          ( newInputLymphDuct->FindImmuneCell(   "macrophageApc"                 )),
    lymphInputdendriticApc           ( newInputLymphDuct->FindImmuneCell(   "dendriticApc"            )),
    lymphInputbCellNaiveRecirculate  ( newInputLymphDuct->FindImmuneCell(   "bCellNaiveRecirculate"   )),
    lymphInputtcEffector  ( newInputLymphDuct->FindImmuneCell(  "tcEffector"    )),
    lymphOutputbCellNaiveRecirculate ( newOutputLymphDuct->FindImmuneCell(  "bCellNaiveRecirculate"  )),
    lymphOutputThNaive               ( newOutputLymphDuct->FindImmuneCell(  "thNaive"                )),
    lymphOutputTcNaive               ( newOutputLymphDuct->FindImmuneCell(  "tcNaive"                )),
    lymphOutputtcEffector ( newOutputLymphDuct->FindImmuneCell(  "tcEffector"    )),
    lymphOutputmacrophageApc         ( newOutputLymphDuct->FindImmuneCell(  "macrophageApc"  )),
    lymphOutputdendriticApc          ( newOutputLymphDuct->FindImmuneCell(  "dendriticApc"  )),

    bloodigM                         ( newbloodReservoir->FindImmuneCell(        "igM"                          )),
    bloodigA                         ( newbloodReservoir->FindImmuneCell(        "igA"                          )),
    bloodigG                         ( newbloodReservoir->FindImmuneCell(        "igG"                          )),
    bloodthEffector       ( newbloodReservoir->FindImmuneCell(     "thEffector"                    )),
    bloodplasmaCell       ( newbloodReservoir->FindImmuneCell(     "plasmaCell"                    )),
    lymphInputthEffector  ( newInputLymphDuct->FindImmuneCell(  "thEffector"    )),
    lymphOutputigM                   ( newOutputLymphDuct->FindImmuneCell(  "igM"                    )),
    lymphOutputigA                   ( newOutputLymphDuct->FindImmuneCell(  "igA"                    )),
    lymphOutputigG                   ( newOutputLymphDuct->FindImmuneCell(  "igG"                    )),
    lymphOutputthEffector ( newOutputLymphDuct->FindImmuneCell(  "thEffector"    )),
    lymphOutputplasmaCell ( newOutputLymphDuct->FindImmuneCell(  "plasmaCell"    ))

{
    double  reservoirVolume, capillaryVolume,lymphInputVolume, organWeight, organVolume;
    int  tissueIndex,i;
    double  balvolume,x1 ;
    double  emptyStrain[TOTALSTRAINS] = {0.0, 0.0,0.0};        
    profileData  emptyProfile[TOTALSTRAINS] = {{1.0, 0.0, 0.0,0.0},{1.0, 0.0, 0.0,0.0},{1.0, 0.0, 0.0,0.0} };
    profileData  prekDendriticInfectionProfile[TOTALSTRAINS] = {{0.0, 0.0, 0.0,0.0},{1.0, 1.0, 0.0,0.0},{0.0, 0.0, 0.0,0.0}};
    profileData  prekDendriticAllergyProfile[TOTALSTRAINS] =   {{0.0, 0.0, 0.0,0.0},{0.0, 0.0, 0.0,0.0},{0.0, 1.0, 0.0, 0.0}};
    double  antigenTestStrain[TOTALSTRAINS] = {0.0, 0.0,0.0};
        
    stepTime = newdTime;
    modelName = newModelName;
    organName = newOrganName;
    organWeight = newWeight ;
    organVolume = newVolume;
    outputLymphDuct = newOutputLymphDuct;
    inputLymphDuct = newInputLymphDuct;
    bloodReservoir = newbloodReservoir;
    capillary = newCapillary;
    capillaryVolume = capillary->ReadVolume('T');
    reservoirVolume = bloodReservoir->ReadVolume('T');
    lymphInputVolume = inputLymphDuct->ReadVolume('T');
    tZoneVolume = 1.0;
    balvolume = epitheliumvolume = 1.0 ;


    if (strcmp(modelName, "lymphNode") == 0) {
        tissueIndex = FindTissueIndex(modelName);
        tZoneVolume = 0.79 * organVolume;
        /* kludge: For memory for now */ 
        // k2LymphOutput_bCellMemory    = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphOutput_bCellMemory  * organWeight,tZoneVolume);       
        // k2LymphOutput_thMemory       = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphOutput_thMemory     * organWeight,tZoneVolume);       
        // k2LymphOutput_tcMemory       = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphOutput_tcMemory     * organWeight,tZoneVolume);       
        k2EffectorKill = CalculateHalfLifeConstant(20.0/60.0) / (8000.0 * tZoneVolume);   
//   k2EffectorKillDendritic = CalculateHalfLifeConstant(24.0) / (8000.0 * tZoneVolume);         
   k2EffectorKillDendritic = CalculateHalfLifeConstant(20.0 / 60.0) / (8000.0 * tZoneVolume);         
  k2ThMemoryActivate = CalculateHalfLifeConstant(0.5);  /* hours, was .5 */ 
        kmThMemoryActivate = CalculateKmConstant(2063.0, tZoneVolume,"ml");
    } /* if */               
    else {
        tissueIndex = FindTissueIndex(organName);
        if (strcmp(modelName, "lymphJunction") == 0) {
            k2LymphJunction = stepTime * newOutputLymphDuct->ReadTimeConstant();
            if (tissueConstants[tissueIndex].k2BloodInput_eosinophil != 0.01234) {
                printf("ERROR, check point mismatch, expected 0.01234 found %g\n",tissueConstants[tissueIndex].k2BloodInput_eosinophil);
                exit(1);
            } /* if */     
        } /* if */
        if (strcmp(modelName, "spleen") == 0) {
            tZoneVolume = 0.55 * 0.25 * organVolume;
        } /* if */    
                  
        if (strcmp(organName, "bronchialTest") == 0) {
            balvolume = 420.0;  /* ul */         
            epitheliumvolume = 600.0;  /* ul */
            // antigenTestStrain[INFLUENZASTRAIN] = 2.9e4 * balvolume; /* 2.9e7particles/ml */
  //          antigenTestStrain[RYEGRASSSTRAIN] = 1.2e8 * 10.0;  // was 1.2e8 * 1.0
  //          antigenTestStrain[RYEGRASSSTRAIN] = 1.2e8 * 1.0;  // was 1.2e8 * 1.0
        } /* if */
        else if (strcmp(organName, "laminaProperiaTest") == 0) {
            balvolume = 1400.0 * LPFRACTION * 1000.0;  /* ul */         
            epitheliumvolume = 2000.0 * LPFRACTION * 1000.0;  /* ul */
             antigenTestStrain[INFLUENZASTRAIN] = 2.9e4 * balvolume; /* 2.9e7particles/ml */
            // antigenTestStrain[RYEGRASSSTRAIN] = 1.2e8;
        } /* elseIf */     
        else {
            epitheliumvolume = 0.4 * organVolume;  /* place holder for now ,ul */
        } /* else */     

        organWeight = 1.0;                              
        /* kludge: For memory for now */ 
        // k2LymphOutput_bCellMemory            = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2LymphOutput_bCellMemory           );
        // k2LymphOutput_thMemory               = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2LymphOutput_thMemory              );
        // k2LymphOutput_tcMemory               = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2LymphOutput_tcMemory              );
        k2EffectorKill = CalculateHalfLifeConstant(20.0/60.0) / (8000.0 * epitheliumvolume);   
//   k2EffectorKillDendritic = CalculateHalfLifeConstant(24.0) / (8000.0 * epitheliumvolume);         
   k2EffectorKillDendritic = CalculateHalfLifeConstant(20.0 / 60.0) / (8000.0 * epitheliumvolume);         
  k2ThMemoryActivate = CalculateHalfLifeConstant(0.5);  /* hours was .5 */ 
        kmThMemoryActivate = CalculateKmConstant(2063.0, epitheliumvolume,"ml");
    } /* else */
              
    printf("%s: volume:%g  tZoneVolume:%g balvolume:%g epitheliumvolume:%g\n",organName,organVolume,tZoneVolume,balvolume, epitheliumvolume);
                             

    /* cell die */                           
    k2DendriticDie = CalculateHalfLifeConstant(3.0 * 24.0);   /* was 169 */ 
    k2MacrophageDie = CalculateHalfLifeConstant(4.0 * 24.0);   /* was 169 */ 
    kHalfLifeTnfAlpha = CalculateHalfLifeConstant(45.0 / 60.0);
    kHalfLifeDendriticApc = CalculateHalfLifeConstant(1.0 * 24.0);
    kHalfLifeInterferonAlpha = CalculateHalfLifeConstant(42.0 / 60.0);
    kHalfLifeIl2 = CalculateHalfLifeConstant(45.0 / 60.0);
    kHalfLifeIgA = CalculateHalfLifeConstant(6.0 * 24.0);
    k2bCellNaiveDie = CalculateHalfLifeConstant(3.0 * 24.0);
    k2thNaiveDie = CalculateHalfLifeConstant(7.7 * 7.0 * 24.0);
    k2tcNaiveDie = CalculateHalfLifeConstant(26.7 * 7.0 * 24.0);
    kHalfLifeGmcsf = CalculateHalfLifeConstant(2.0) ;      
    kHalfLifebCellApc = CalculateHalfLifeConstant(3.0 * 24.0);                 
    kHalfLifebCellApcMemory = CalculateHalfLifeConstant(3.0 * 24.0);                 
    kHalfLifebCellCentroblast = CalculateHalfLifeConstant(20.0  );         
    kHalfLifeThGerminalCenter = CalculateHalfLifeConstant(8.0) ; 
    kHalfLifePlasmaCell = CalculateHalfLifeConstant(3.0 * 7.0 * 24.0) ;
    kHalfLifeMacrophageApc = CalculateHalfLifeConstant(1.0 * 24.0) ;          
    kHalfLifebCellCentrocyteInitial = CalculateHalfLifeConstant(8.0);   
    kHalfLifebCellCentrocyteApc = CalculateHalfLifeConstant(8.0);       
    kHalfLifebCellPlasmaMedullary = CalculateHalfLifeConstant(3.0 * 24.0);
    kibCellRecirculateDie = tissueConstants[tissueIndex].numberOfBCellsNaive[BACKGROUNDSTRAIN] * organWeight;
    k2bCellRecirculateDie  =  CalculateHalfLifeConstant(4.5 * 7.0 * 24.0) / kibCellRecirculateDie ;

    /* cell creation */ 
    kGenerateMonocyte =  CalculateK2Constant(4446.0);         
    knGenerateMonocyte = 2.0;                                     
    kmGenerateMonocyte = CalculateKmConstant(2.0e-9, reservoirVolume,"ml");              
    kGenerateGmcsf = CalculateK2Constant(1.3e4 / 6.02e17);   /* umoles/sec */            
    kGenerateBCells =    CalculateK2Constant(3.0e10 / (24.0 * 3600.0));
    kGenerateThCells =   CalculateK2Constant(0.78 * 0.007 * 1.2e12 / (24.0 * 3600.0));
    kGenerateTcCells =   CalculateK2Constant(0.22 * 0.007 * 1.2e12 / (24.0 * 3600.0));
    kGeneratePlatelets = CalculateK2Constant(1.9e6);
    kGenerateRbc =       CalculateK2Constant(1.8e6);       
    k2IgaProduction = CalculateK2Constant(1.3e4 / 6.02e17);   /* umoles/sec */            
    k2PlasmaMedullary2IgM = CalculateK2Constant(2.0e3 / 6.02e17);   /* umoles/sec */              
    kGenerateTnfAlpha = CalculateK2Constant(155 / 6.02e17);   /* umoles/sec-cell */            
    k2BlastIl2 = CalculateK2Constant(300.0 / 6.02e17);  /* umoles/sec-cell */
    k2EffectorPrecursorIl2 = CalculateK2Constant(300.0 / 6.02e17);    /* umoles/sec-cell */ 
                                                        

    /* cell migration */ 
    k2BloodInput_bCellNaiveRecirculate = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_bCellNaiveRecirculate * organWeight, reservoirVolume);
    k2BloodInput_bCellNaive            = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_bCellNaive            * organWeight, reservoirVolume);
    k2BloodInput_thNaive               = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_thNaive               * organWeight, reservoirVolume);
    k2BloodInput_tcNaive               = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_tcNaive               * organWeight, reservoirVolume);
    k2BloodInput_tcEffector = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_tcEffector * organWeight, reservoirVolume);
    k2BloodInput_thEffector = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_thEffector * organWeight, reservoirVolume);
    k2BloodInput_Dendritic  = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_Dendritic             * organWeight, capillaryVolume);
    k2BloodInput_rbc        = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_rbc        * organWeight, capillaryVolume);
    k2BloodInput_platelets  = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_platelets  * organWeight, capillaryVolume);
    k2BloodInput_Macrophage = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_Macrophage * organWeight, capillaryVolume);
    k2BloodInputPlasmaCell = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_plasmaCell  * organWeight, reservoirVolume); 

    k2BloodInput_bCellMemory              = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_bCellMemory               * organWeight, reservoirVolume);
    k2BloodInput_thMemory                 = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_thMemory                  * organWeight, reservoirVolume);
    k2BloodInput_tcMemory                 = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_tcMemory                  * organWeight, reservoirVolume);

    k2BloodOutput_bCellNaive = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2BloodOutput_bCellNaive);
    k2BloodOutput_bCellNaiveRecirculate = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2BloodOutput_bCellNaiveRecirculate);
    k2BloodOutput_thNaive               = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2BloodOutput_thNaive              );
    k2BloodOutput_tcNaive               = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2BloodOutput_tcNaive              );

    k2BloodOutput_bCellMemory               = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2BloodOutput_bCellMemory            );
    k2BloodOutput_thMemory                  = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2BloodOutput_thMemory               );
    k2BloodOutput_tcMemory                  = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2BloodOutput_tcMemory               );

    k2LymphInput_bCellNaiveRecirculate = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphInput_bCellNaiveRecirculate * organWeight, lymphInputVolume);
    k2LymphInput_macrophageApc = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphInput_macrophageApc * organWeight, lymphInputVolume);
    k2LymphInput_dendriticApc  = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphInput_dendriticApc  * organWeight, lymphInputVolume);

    k2LymphInput_bCellMemory  = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphInput_bCellMemory  * organWeight, lymphInputVolume);
    k2LymphInput_thMemory     = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphInput_thMemory     * organWeight, lymphInputVolume);
    k2LymphInput_tcMemory     = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphInput_tcMemory     * organWeight, lymphInputVolume);

    k2LymphOutput_bCellNaiveRecirculate = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2LymphOutput_bCellNaiveRecirculate);
    k2LymphOutput_tcEffector = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphOutput_tcEffector * organWeight,tZoneVolume);
    k2LymphOutput_thEffector = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphOutput_thEffector * organWeight,tZoneVolume);
    k2LymphOutput_macrophageApc         = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphOutput_macrophageApc,epitheliumvolume        );
    k2LymphOutput_dendriticApc          = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphOutput_dendriticApc,epitheliumvolume         );
    k2LymphOutput_thNaive               = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2LymphOutput_thNaive              );
    k2LymphOutput_tcNaive               = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2LymphOutput_tcNaive              );
    k2LymphOutput_plasmaCell = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2LymphOutput_plasmaCell * organWeight,tZoneVolume);      
    k2LymphOutput_igM = CalculateMigrateFlowConstant(0.05 * organWeight,tZoneVolume); 
    k2LymphOutput_bCellMemory            = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2LymphOutput_bCellMemory           );
    k2LymphOutput_thMemory               = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2LymphOutput_thMemory              );
    k2LymphOutput_tcMemory               = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2LymphOutput_tcMemory              );
               

    /* bronchial tissue constants */
    k2MucociliaryClearance =  CalculateHalfLifeConstant(14.0);
    knInfluenzaNeutralize = 10.0 / 6.02e17;
    k2InfluenzaNeutralize = CalculateHalfLifeConstant(1.1) / (1.7e-10 * balvolume);
    k2EpitheliaReplication = CalculateHalfLifeConstant(5.0);
    k2EpitheliaInfection = CalculateHalfLifeConstant(1.7) / (1.0e7 * balvolume);
    knEpitheliaInfection = 10.0;
    k2EpitheliaResistive = CalculateHalfLifeConstant(1.0) / (0.05 * epitheliumvolume);
    knEpitheliaResistive = 1.3e-7;  /* iu */
    k2EpitheliaDie = CalculateHalfLifeConstant(30.0);
    k2EpitheliaResistiveDie = CalculateHalfLifeConstant(24.0);
    k2EpitheliaApcDie = CalculateHalfLifeConstant(16.0);
    k2VirusReplication = CalculateK2Constant(7000.0 / (24.0 * 3600.0));
    knEffectorKill = 0.05;  // was 0.1
    k2MacrophageInfection = CalculateHalfLifeConstant(1.0) / (1.0e7 * balvolume);
    knMacrophageInfection = 5.0;
    k2GenerateInterferonAlpha = CalculateK2Constant(2.0e-4 / (24.0 * 3600.0));
    k2DendriticInfection = CalculateHalfLifeConstant(1.0) / (1.0e7 * balvolume);
    knDendriticInfection = 5.0;
    k2macrophageReplicate = CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2macrophageReplicate);
    k2DendriticReplicate =  CalculateHalfLifeConstant(tissueConstants[tissueIndex].k2DendriticReplicate);
  knInflammatory = 160.0  ;      // was 4.0
//  knInflammatory = 4.0  ;      // was 4.0
  knMonocyteInflammatory = 160.0  ;      // was 4.0
    kmInflammatory = CalculateKmConstant(3.0e-7, epitheliumvolume,"ml");
  k2TcEffector2Memory = CalculateHalfLifeConstant(0.05 * 6.0 * 7.0 * 24.0);  /* hours */ 
    kmTcEffector2Memory = CalculateKmConstant(1.0e4, epitheliumvolume,"ml");
  k2ThEffector2Memory = CalculateHalfLifeConstant(0.05 * 6.0 * 7.0 * 24.0);  /* hours */ 
    kmThEffector2Memory = CalculateKmConstant(1.0e4, epitheliumvolume,"ml");
    knInflammatoryDendriticOutput = 4.0 ;    /* estimate 4 now */ 
    knInflammatoryOutput = 10.0 ;    /* estimate 4 now */ 
    kmInflammatoryOutput = CalculateKmConstant(3.0e-7, epitheliumvolume,"ml");
    k2tcAicd = CalculateHalfLifeConstant(9.2);
    kmtcAicd = CalculateKmConstant(121.90, epitheliumvolume,"ml");
    k0tcAicd = CalculateHalfLifeConstant(1.0 * 20.0);
    k2thAicd = CalculateHalfLifeConstant(9.2);
    kmthAicd = CalculateKmConstant(121.90, epitheliumvolume,"ml");
    k0thAicd = CalculateHalfLifeConstant(1.0 * 20.0);
       
    /* lymphNode/spleen constants */
    /* lymphNode/spleen constants: tc cells */
    k2TcNaiveActivate = CalculateHalfLifeConstant(3.14);  /* hours */ 
    kmTcNaiveActivate = CalculateKmConstant(2063.0, tZoneVolume,"ml");
    k2TcBlastPrecursorActivate = 0.95;
    kmTcBlastPrecursorActivate = CalculateKmConstant(457.0, tZoneVolume,"ml");
    k2TcPrecursorCount = CalculateK2Constant(6.4e-5);
    kmTcPrecursorCount = CalculateKmConstant(2.1e-8, tZoneVolume,"ml");
    kTcBlastReplicate = 0.6;      /* dispersion variance */            
    k2EffectorPrecursorIl2Autocrine = CalculateHalfLifeConstant(45.0) / (2.0e4 * tZoneVolume);   /* thl = 45 hours @ blastcount = 2.0e7/ml */ 
    k2TcMemoryActivate = CalculateHalfLifeConstant(1.0);  /* hours */ 
    kmTcMemoryActivate = CalculateKmConstant(2063.0, tZoneVolume,"ml");
    k2TcPrecursorCountMemory = CalculateK2Constant(6.4e-5);
    kmTcPrecursorCountMemory = CalculateKmConstant(2.1e-8, tZoneVolume,"ml");
    kTcBlastReplicateMemory = 0.6;      /* dispersion variance */            
                
    /* lymphNode/spleen constants: th cells */
    k2ThNaiveActivate = CalculateHalfLifeConstant(3.14);            
    kmThNaiveActivate = CalculateKmConstant(2063.0, tZoneVolume,"ml");            
    k2thBlastPrecursorActivate = 0.95;   
    kmthBlastPrecursorActivate = CalculateKmConstant(457.0, tZoneVolume,"ml");   
    k2thPrecursorCount = CalculateK2Constant(6.4e-5);           
    kmthPrecursorCount = CalculateKmConstant(2.1e-8, tZoneVolume,"ml");           
    kthBlastReplicate = 0.6;            
#if 0
    k2PolarizationTh1 = 0.15;            
    kmPolarizationTh1 = CalculateKmConstant(1.0e4, tZoneVolume,"ml");            
    k2PolarizationTh2 = 0.06;            
    kmPolarizationTh2 = CalculateKmConstant(1.0e4, tZoneVolume,"ml");            
#endif
    k2PolarizationTh1 = 0.09;  // was .15          
    kmPolarizationTh1 = CalculateKmConstant(1.0e2, tZoneVolume,"ml");            
    k2PolarizationTh2 = 0.025;  // was 0.06          
    kmPolarizationTh2 = CalculateKmConstant(1.0e2, tZoneVolume,"ml");            

    k2ThPrecursorCountMemory = CalculateK2Constant(6.4e-5);
    kmThPrecursorCountMemory = CalculateKmConstant(2.1e-8, tZoneVolume,"ml");
    kthBlastReplicateMemory = 0.6;      /* dispersion variance */            

    /* lymphNode/spleen constants: b cells */
    kibCellNaiveFollicle =  tissueConstants[tissueIndex].numberOfBCellsRecirculate[BACKGROUNDSTRAIN] * organWeight;
    k2bCellNaiveFollicle  = 2.0 * kibCellNaiveFollicle  * CalculateHalfLifeConstant(4.5 * 7.0 * 24.0) ;
    k2bCellNaiveRecirculateActivate = CalculateHalfLifeConstant(3.0); /* gives: t half life = 6 hours @ dendritic = 1,000/ml */ 
    kmbCellNaiveRecirculateActivate = CalculateKmConstant(1000.0, tZoneVolume,"ml"); 
    k2bCellApcActivate = CalculateHalfLifeConstant(2.0);                
    kmbCellApcActivate = CalculateKmConstant(1.0e5, tZoneVolume,"ml");                
    kbCentroblastReplicateInitial = 0.05;                         
    kbCentroblastReplicate = 1.0;            

#if 0               
    k2SwitchesIgg = 0.142;                
    kmSwitchesIgg = CalculateKmConstant(1.0e5, tZoneVolume,"ml");                
    k2SwitchesIga = 0.038;                
    kmSwitchesIga = CalculateKmConstant(1.0e4, tZoneVolume,"ml");                
#endif
    k2SwitchesIgg = 0.22;  // was .142              
    kmSwitchesIgg = CalculateKmConstant(1.0e5, tZoneVolume,"ml");                
    k2SwitchesIga = 0.038;  // was .038              
    kmSwitchesIga = CalculateKmConstant(1.0e2, tZoneVolume,"ml");                
    kiSwitchesIga = CalculateKmConstant(1.0e3, tZoneVolume,"ml");                
    k2SwitchesIgg1 = 0.22;  // was .142              
    kmSwitchesIgg1 = CalculateKmConstant(1.0e5, tZoneVolume,"ml");                
    k2SwitchesIge = 0.11;  // was .142              
    kmSwitchesIge = CalculateKmConstant(1.0e5, tZoneVolume,"ml");                

  k2bCellMemoryMarginalActivate = CalculateHalfLifeConstant(3.0 / 10.0);
  kmbCellMemoryMarginalActivate = CalculateKmConstant(10000.0, tZoneVolume,"ml"); 

    k2bCellMemoryActivate = CalculateHalfLifeConstant(3.0 / 10.0);
    kmbCellMemoryActivate = CalculateKmConstant(1000.0, tZoneVolume,"ml"); 

    k2bCellApcMemoryActivate = CalculateHalfLifeConstant(2.0 / 4.0);                
    kmbCellApcMemoryActivate = CalculateKmConstant(1.0e5, tZoneVolume,"ml");                
    kbCentroblastReplicateInitialMemory = 0.05;                         

    /* lymphNode/spleen constants: b cells (red pulp, medullary)*/
    kbPlasmaReplicateInitial = 1.0 - kbCentroblastReplicateInitial;                 
    kbPlasmaReplicateInitialMemory = 1.0 - kbCentroblastReplicateInitialMemory;                 
    kbPlasmaReplicate = 0.6;                 
 kbPlasmaReplicateDecision = (2.0 - 0.2);  // was 2.0 - 0.1
                   
    /* lymphNode/spleen constants: b cells, miscellaneous (germinal center) */
    k2Centroblast2Centrocyte = CalculateHalfLifeConstant(4.85);
    k2bCellCentrocyteInitialActivate = CalculateHalfLifeConstant(8.0);  
    kmbCellCentrocyteInitialActivate = CalculateKmConstant(7.5, 1.0,"ul");  
    knbCellCentrocyteInitialActivate = 0.01;
    k2bCellCentrocyteActivate = CalculateHalfLifeConstant(2.0);         
    kmbCellCentrocyteActivate = CalculateKmConstant(150.0, 1.0,"ul");         
    k2Centrocyte2Centroblast = CalculateHalfLifeConstant(28.0 / 60.0);
    k2Centrocyte2PlasmaCell = CalculateHalfLifeConstant(2.4) ;
    k2Centrocyte2bCellMemory = CalculateHalfLifeConstant(1.6) ;
  k2Centrocyte2bCellMemoryMarginal = CalculateHalfLifeConstant(3.0 * 16.0) ;
    k2Effector2GerminalCenter = CalculateHalfLifeConstant(2.0) ; 
    k2FdcApc = CalculateHalfLifeConstant(30.0 / 60.0);
    kmFdcApc = CalculateKmConstant(75000.0, 1.0,"ul");          
    knFdcApc = 1.0 / knbCellCentrocyteInitialActivate;                                                         
// knMacrophageApc = 10;                                         
 knMacrophageApc = 2;          /* was 1 */                                
    k2immuneComplex = CalculateHalfLifeConstant(10.0 / 60.0) / (1.7e-10 * tZoneVolume);                 
    knimmuneComplex = 1.0 / 6.02e17;                 

    GenericImmuneCell::CopyProfile(kDendriticInfectionProfile, prekDendriticInfectionProfile );

    /* counters */ 
    numberOfGerminalCenters = 0.001;
    thBlastCount = 0.0;
    thBlastDCount =  CalculateK2Constant(1.0 / (3.0 * 3600.0));
    bBlastCount = 0.0;                       
    bBlastDCount =  CalculateK2Constant(1.0 / (6.0 * 3600.0));                      
    bPlasmaCount = 0.0;                      
    bPlasmaDCount =  CalculateK2Constant(1.0 / (3.6 * 3600.0));  /* minimum replication time */                    
    tcBlastCount = 0.0;
    tcBlastDCount =  CalculateK2Constant(1.0 / (3.0 * 3600.0));
    adjustTcBlast = 0.0;
    adjustTcBlastMemory = 0.0;
    inflammatoryRate = 0.0;             
    inflammatoryMonocyteRate = 0.0;             
    inflammatoryOutputRate = 0.0;
    il3inflammatoryRate = 0.0;            
    il5inflammatoryRate = 0.0;            
    thMemoryActivateCount = 0.0;          
    dthMemoryActivateCount =  CalculateK2Constant(1.0 / (0.8 * 3600.0));          
                      
    /* initialize cells */ 
    antigen.ResetImmuneCell (  emptyStrain,      emptyProfile,            "antigen"             , newOrganName);                         
    antigenBal.ResetImmuneCell (antigenTestStrain  , emptyProfile , "antigenBal"            , newOrganName);
    bCellNaive.ResetImmuneCell (  BuildStrain(tissueConstants[tissueIndex].numberOfBCellsNaive , organWeight), emptyProfile  ,      "bCellNaive"             , newOrganName);
    bCellNaiveRecirculate.ResetImmuneCell (  BuildStrain(tissueConstants[tissueIndex].numberOfBCellsRecirculate , organWeight), emptyProfile , "bCellNaiveRecirculate"  , newOrganName);
    bCellNaiveMarginalZone.ResetImmuneCell (  BuildStrain(tissueConstants[tissueIndex].numberOfBCellsMarginalZone , organWeight), emptyProfile, "bCellNaiveMarginalZone"      , newOrganName);
    bCellCentrocyteApc.ResetImmuneCell (  emptyStrain,      emptyProfile,    "bCellCentrocyteApc"     , newOrganName);                
    bCellPlasmaMedullary.ResetImmuneCell (  emptyStrain,      emptyProfile,  "bCellPlasmaMedullary"   , newOrganName);              
    bCellApc.ResetImmuneCell (  emptyStrain,      emptyProfile,              "bCellApc"               , newOrganName);
    bCellDeadCentroblast.ResetImmuneCell (  emptyStrain,      emptyProfile,              "bCellApc"               , newOrganName);
    bCellCentroblast.ResetImmuneCell ( emptyStrain , emptyProfile,  "bCellCentroblast"       , newOrganName);
    bCellCentrocyteInitial.ResetImmuneCell (  emptyStrain, emptyProfile,                                    "bCellCentrocyteInitial" , newOrganName);
    bCellCentrocyte.ResetImmuneCell (  emptyStrain,   emptyProfile,                                  "bCellCentrocyte"        , newOrganName);
    bCellBlast.ResetImmuneCell (  emptyStrain,      emptyProfile,            "bCellBlast"             , newOrganName);                        
    for (i = 0; i < NUMBEROFBCENTROBLASTPRECURSOR; i++) {                                
        bCentroblastPrecursor[i].ResetImmuneCell (  emptyStrain, emptyProfile , "bCentroblastPrecursor"            , newOrganName);
    } /* iForLoop */                                        
    for (i = 0; i < NUMBEROFBPLASMAPRECURSOR; i++) {                                
        bPlasmaPrecursor[i].ResetImmuneCell (  emptyStrain, emptyProfile , "bPlasmaPrecursor"            , newOrganName);
    } /* iForLoop */                                        


    histamine = 0.0;                      
    mastCellNaive = tissueConstants[tissueIndex].numberOfmastCell * organWeight;                  
    eosinophil = tissueConstants[tissueIndex].numberOfeosinophil * organWeight;                     
    ltc4 = 0.0;                           
    fev1 = 100.0;                           
    il3 = 0.0;                            
    il5 = 0.0;                            
    dendriticImmature = tissueConstants[tissueIndex].numberOfDendritic * organWeight;
    dendriticImmatureInitial = dendriticImmature;
    dendriticApc.ResetImmuneCell (  emptyStrain,       emptyProfile,                              "dendriticApc"           , newOrganName);
    epitheliaResistive = 0.0;
    epitheliaApc = 0.0;
    epitheliaDead = 0.0;
    epitheliaCell = tissueConstants[tissueIndex].epitheliaCell * organWeight;
    fdcApc.ResetImmuneCell (  emptyStrain,      emptyProfile,                               "fdcApc"                 , newOrganName);
    fdcGerminalCenters = tissueConstants[tissueIndex].fdcGerminalCenters *  organWeight; 
    interferonAlpha = 0.0;
    igM.ResetImmuneCell (  emptyStrain,      emptyProfile,            "igM"             , newOrganName);                             
    igaBal.ResetImmuneCell ( emptyStrain , emptyProfile , "igaBal"            , newOrganName);
    il2 = 0.0;
    immuneComplex.ResetImmuneCell (  emptyStrain,      emptyProfile,            "immuneComplex"             , newOrganName);                   
    macrophage = tissueConstants[tissueIndex].numberOfMacrophage * organWeight ;
    macrophageInitial = macrophage;
    macrophageApc.ResetImmuneCell (  emptyStrain,      emptyProfile,   "macrophageApc"  , newOrganName);
    plasmaCell.ResetImmuneCell (  emptyStrain,      emptyProfile,            "plasmaCell"             , newOrganName);
    tnfAlpha = 0.0;
    tcPrecursorCount = 0.0;
    thPrecursorCount = 0.0;
    thEffectorPrecursorTotal = 0.0;          
    th2EffectorPrecursorTotal = 0.0;         
    thEffectorPrecursorTotalMemory = 0.0;     
    th2EffectorPrecursorTotalMemory = 0.0;    
    tcPrecursorCountMemory = 0.0;             
    thPrecursorCountMemory = 0.0;             
    tcBlastPrecursorTotal = 0.0 ;
    thBlastPrecursorTotal = 0.0 ;
    tcBlast.ResetImmuneCell (  emptyStrain, emptyProfile , "tcBlast"            , newOrganName);
    tcAnergy.ResetImmuneCell (  emptyStrain, emptyProfile , "tcAnergy"            , newOrganName);
    tcEffector.ResetImmuneCell (  emptyStrain, emptyProfile , "tcEffector"            , newOrganName);
    thEffector.ResetImmuneCell (  emptyStrain,      emptyProfile,            "thEffector"             , newOrganName);
    thBlast.ResetImmuneCell (  emptyStrain,      emptyProfile,               "thBlast"                , newOrganName) ;
    thAnergy.ResetImmuneCell (  emptyStrain,      emptyProfile,              "thAnergy"               , newOrganName);
    thGerminalCenter.ResetImmuneCell (  emptyStrain,      emptyProfile,      "thGerminalCenter"       , newOrganName);                  
    thNaive.ResetImmuneCell (  BuildStrain(tissueConstants[tissueIndex].numberOfThCellsNaive , organWeight),  emptyProfile,       "thNaive"                , newOrganName);
    tcNaive.ResetImmuneCell (  BuildStrain(tissueConstants[tissueIndex].numberOfTcCellsNaive , organWeight),  emptyProfile,       "tcNaive"                , newOrganName);
    for (i = 0; i < NUMBEROFTCBLASTPRECURSOR; i++) {
        tcBlastPrecursor[i].ResetImmuneCell (  emptyStrain, emptyProfile , "tcBlastPrecursor"            , newOrganName);
    } /* iForLoop */
    for (i = 0; i < NUMBEROFTCEFFECTORPRECURSOR; i++) {
        tcEffectorPrecursor[i].ResetImmuneCell (  emptyStrain, emptyProfile , "tcEffectorPrecursor"            , newOrganName);
    } /* iForLoop */
    for (i = 0; i < NUMBEROFTHBLASTPRECURSOR; i++) {
        thBlastPrecursor[i].ResetImmuneCell (  emptyStrain, emptyProfile , "thBlastPrecursor"            , newOrganName);
    } /* iForLoop */
    for (i = 0; i < NUMBEROFTHEFFECTORPRECURSOR; i++) {
        thEffectorPrecursor[i].ResetImmuneCell (  emptyStrain, emptyProfile , "thEffectorPrecursor"            , newOrganName);
    } /* iForLoop */
    virtualThEffector.ResetImmuneCell (  emptyStrain,      emptyProfile,     "virtualThEffector"      , newOrganName);                 

    mastCellDegranulate.ResetImmuneCell (  emptyStrain,      emptyProfile,      "mastCellDegranulate"       , newOrganName);                  
    ige.ResetImmuneCell (  emptyStrain,      emptyProfile,      "ige"       , newOrganName);                  
    for (i = 0; i < NUMBEROFTHMEMORYACTIVATE; i++) {
        thMemoryBlast[i].ResetImmuneCell (  emptyStrain, emptyProfile , "thMemoryBlast"            , newOrganName);
    } /* iForLoop */

    bCellMemory.ResetImmuneCell (  emptyStrain, emptyProfile , "bCellMemory"            , newOrganName);
    bCellMemoryMarginal.ResetImmuneCell (  emptyStrain, emptyProfile , "bCellMemoryMarginal"            , newOrganName);
    tcMemory.ResetImmuneCell (  emptyStrain, emptyProfile , "tcMemory"            , newOrganName);
    tcBlastMemory.ResetImmuneCell (  emptyStrain, emptyProfile , "tcBlastMemory"            , newOrganName);
    thBlastMemory.ResetImmuneCell (  emptyStrain, emptyProfile , "thBlastMemory"            , newOrganName);
    virtualThEffectorMemory.ResetImmuneCell (  emptyStrain, emptyProfile , "virtualThEffectorMemory"            , newOrganName);
    bCellApcMemory.ResetImmuneCell (  emptyStrain, emptyProfile , "bCellApcMemory"            , newOrganName);
    bCellBlastMemory.ResetImmuneCell (  emptyStrain, emptyProfile , "bCellBlastMemory"            , newOrganName);
    for (i = 0; i < NUMBEROFTHEFFECTORPRECURSORMEMORY; i++) {
        thEffectorPrecursorMemory[i].ResetImmuneCell (  emptyStrain, emptyProfile , "thEffectorPrecursorMemory"            , newOrganName);
    } /* iForLoop */             
    for (i = 0; i < NUMBEROFTCEFFECTORPRECURSORMEMORY; i++) {
        tcEffectorPrecursorMemory[i].ResetImmuneCell (  emptyStrain, emptyProfile , "tcEffectorPrecursorMemory"            , newOrganName);
    } /* iForLoop */             

    mastCell.ResetImmuneCell (  emptyStrain,      emptyProfile,      "mastCell"       , newOrganName);                  
    thMemory.ResetImmuneCell (  emptyStrain, emptyProfile , "thMemory"            , newOrganName);
// mastCell.AddStrain(RYEGRASSSTRAIN, igeProfileGlobal ,3.0e5);      // 4.4e5
// thMemory.AddStrain(RYEGRASSSTRAIN,  th2ProfileGlobal,5.0e3);   // was 11e3

    kHalfLifeil3 = CalculateHalfLifeConstant(35.0 / 60.0);                   
    kHalfLifeil5 = CalculateHalfLifeConstant(45.0 / 60.0);                   
    kGenerateeosinophil =  CalculateK2Constant(21393.0);                       
    knGenerateeosinophil = 3.0;                                               
    kmGenerateeosinophil = CalculateKmConstant(3.3e-8, reservoirVolume,"ml"); 
    kGeneratemastCell =  CalculateK2Constant(160.0);                       
    knGeneratemastCell = 1.0;                                               
    kmGeneratemastCell = CalculateKmConstant(1.1e-7, reservoirVolume,"ml"); 
    kHalfLifeIgE = CalculateHalfLifeConstant(2.0 * 24.0);                   
    knInflammatoryil3 = 4.0 / CalculateKmConstant(1.1e-7, epitheliumvolume,"ml");              
    knInflammatoryil5 = 5.0 / CalculateKmConstant(3.3e-8, epitheliumvolume,"ml");              
    k2IgeProduction = CalculateK2Constant(1.1e4 / 6.02e17);   /* umoles/sec */ 

  x1 = CalculateKmConstant(1000.0, epitheliumvolume,"ml");   /* was 1,000 */ 
    kGenerateIl3 = CalculateK2Constant(6000.0 / 6.02e17) / x1;   /* umoles/sec */                    
    kGenerateIl5 = CalculateK2Constant(9600.0 / 6.02e17) / x1;   /* umoles/sec */   // was 1460                
    kHalfLifehistamine = CalculateHalfLifeConstant(13.0 / 60.0);  // was 15, 25, 40.0           
    k2mastCellAllergy = CalculateHalfLifeConstant(5.0 / 60.0) / (1.2e8 * balvolume); // was 5.8, 58.0  
    kn1mastCellAllergy = 1.6e10 / 6.02e17;             
    kn2mastCellAllergy = 30.0e3;             
    k2mastCellNaive = CalculateHalfLifeConstant(1.1) / (1.7e-10 * balvolume); 
    knmastCellNaive = 3.0e5 / 6.02e17; 
    kHalfLifemastCellNaive = CalculateHalfLifeConstant(20.0 * 24.0);
    kHalfLifemastCellDegranulate = CalculateHalfLifeConstant(1.0 * 24.0);
    kHalfLifemastCell = CalculateHalfLifeConstant(20.0 * 24.0);
    k2BloodInput_mastCell = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_mastCell * organWeight, capillaryVolume); ;          
    k2BloodInput_eosinophil = CalculateMigrateFlowConstant(tissueConstants[tissueIndex].k2BloodInput_eosinophil * organWeight, capillaryVolume); ;        
    x1 = CalculateKmConstant(12.0 * 3.3e-8, epitheliumvolume,"ml");               
    k2eosinophilLtc4 = CalculateK2Constant( 200.0 / 6.02e17) / (x1 * x1 * x1 * x1);   /* umoles/sec */                
    kHalfLifeltc4 = CalculateHalfLifeConstant(20.0 / 60.0);
    kHalfLifeeosinophil = CalculateHalfLifeConstant(11.0 * 7.0 * 24.0);
    kltc4multiplier = 500.0;                
    k2fev1 = .57; /* mild asthma */                         
    kmfev1 = CalculateKmConstant(4.5e-5, epitheliumvolume,"ml");  /* 5 ng/ml */ 
    GenericImmuneCell::CopyProfile(kDendriticAllergyProfile, prekDendriticAllergyProfile );
    kthBlastActivateMemory  = 0.6;
    kTransferil3 = CalculateHalfLifeConstant(15.0 / 60.0);
    kTransferil5 = CalculateHalfLifeConstant(15.0 / 60.0);
}       
                                       
              
                       
void  GenericImmuneTissue::ExecuteBronchialTest ()
{
    double  rate,x1;
    int  i ;    
    
    /* bal equations */
    antigenBal.MigrateOutput(k2MucociliaryClearance);

    rate = antigenBal.ReadValue(INFLUENZASTRAIN);
// rate=0.0;
    if (rate > 1.0e-10) {        /* hack, when antigen is essentially gone, don't evaluate  */ 
        rate *= k2InfluenzaNeutralize * igaBal.ReadValue(INFLUENZASTRAIN);
        antigenBal.AddStrain(INFLUENZASTRAIN, -rate);
        igaBal.AddStrain(INFLUENZASTRAIN, -rate * knInfluenzaNeutralize);
    } /* if */     

    igaBal.MigrateOutput(kHalfLifeIgA);
    ige.MigrateOutput(kHalfLifeIgE);

    /* Epithelia equations */
    rate = k2EpitheliaReplication  * epitheliaDead;
    epitheliaDead -= rate;
    epitheliaCell += rate;      /* replication/fibroblasts */

    rate = k2EpitheliaInfection * epitheliaCell * antigenBal.ReadValue(INFLUENZASTRAIN) ;
    epitheliaCell -= rate ;
    epitheliaApc += rate ;
    antigenBal.AddStrain(INFLUENZASTRAIN, -rate * knEpitheliaInfection);

    rate = k2EpitheliaResistive * epitheliaCell * interferonAlpha ;
    epitheliaResistive += rate ;
    epitheliaCell -= rate ;
    interferonAlpha -= rate * knEpitheliaResistive;

    rate = k2EpitheliaDie * epitheliaCell ;
    epitheliaCell -= rate ;
    epitheliaDead += rate;

    rate = k2EpitheliaResistiveDie * epitheliaResistive ;
    epitheliaResistive -= rate ;
    epitheliaCell += rate;

    rate = k2VirusReplication * epitheliaApc ;
    antigenBal.AddStrain(INFLUENZASTRAIN, rate);
    rate = k2EpitheliaApcDie * epitheliaApc ;
    epitheliaApc -= rate ;
    epitheliaDead += rate;

    rate = k2EffectorKill * epitheliaApc * tcEffector.ReadValue(INFLUENZASTRAIN) ;
    epitheliaApc -= rate ;
    epitheliaDead += rate;
    tcEffector.AddStrain(INFLUENZASTRAIN, -rate * knEffectorKill);

    tcEffector.MigrateAicd(dendriticApc, k2tcAicd,kmtcAicd,k0tcAicd); 
    thEffector.MigrateAicd(dendriticApc, k2thAicd,kmthAicd,k0thAicd); 
    tcEffector.ApcDeActivate(tcMemory,dendriticApc, k2TcEffector2Memory,kmTcEffector2Memory);
    thEffector.ApcDeActivate(thMemory,dendriticApc, k2ThEffector2Memory,kmThEffector2Memory);

    rate = k2MacrophageInfection * macrophage * antigenBal.ReadValue(INFLUENZASTRAIN) ;
    macrophage -= rate ;
    macrophageApc.AddStrain(INFLUENZASTRAIN, rate);
    antigenBal.AddStrain(INFLUENZASTRAIN, -rate * knMacrophageInfection);

    rate = k2GenerateInterferonAlpha * macrophageApc.ReadTotal() ;
    interferonAlpha += rate;                  

    rate = interferonAlpha * kHalfLifeInterferonAlpha;
    interferonAlpha -= rate;

    /* Interstitium equations */                                            
    il3inflammatoryRate = 1.0 + knInflammatoryil3 * il3;
    il5inflammatoryRate = 1.0 + knInflammatoryil5 * il5;
    inflammatoryRate = 1.0 + knInflammatory * tnfAlpha / (kmInflammatory + tnfAlpha);
    inflammatoryMonocyteRate = 1.0 + knMonocyteInflammatory * tnfAlpha / (kmInflammatory + tnfAlpha);
    inflammatoryOutputRate = 1.0 + knInflammatoryOutput * tnfAlpha / (kmInflammatoryOutput + tnfAlpha);
    inflammatoryDendriticOutputRate = 1.0 + knInflammatoryDendriticOutput * tnfAlpha / (kmInflammatoryOutput + tnfAlpha);
    
    rate = k2DendriticInfection * dendriticImmature * antigenBal.ReadValue(INFLUENZASTRAIN) ;
    dendriticImmature -= rate ;
    dendriticApc.AddStrain(INFLUENZASTRAIN, kDendriticInfectionProfile, rate);
    antigenBal.AddStrain(INFLUENZASTRAIN, -rate * knDendriticInfection);

    x1 = antigenBal.ReadValue(RYEGRASSSTRAIN) ;
    if (x1 > 1.0e-10) {  /* hack, don't evaluate if antigen almost gone */ 
        rate = k2DendriticInfection * dendriticImmature * antigenBal.ReadValue(RYEGRASSSTRAIN) ;
        dendriticImmature -= rate ;
        dendriticApc.AddStrain(RYEGRASSSTRAIN, kDendriticAllergyProfile, rate);
        //  dendriticApc.Snapshot();
        antigenBal.AddStrain(RYEGRASSSTRAIN, -rate * knDendriticInfection);
    
        rate = k2MacrophageInfection * macrophage * antigenBal.ReadValue(RYEGRASSSTRAIN) ;
        macrophage -= rate ;
        macrophageApc.AddStrain(RYEGRASSSTRAIN, rate);
        antigenBal.AddStrain(RYEGRASSSTRAIN, -rate * knMacrophageInfection);
    
        rate = k2mastCellAllergy * mastCell.ReadValue(RYEGRASSSTRAIN) * antigenBal.ReadValue(RYEGRASSSTRAIN) ;
        mastCell.AddStrain(RYEGRASSSTRAIN, -rate);              
        mastCellDegranulate.AddStrain(RYEGRASSSTRAIN, igeProfileGlobal ,rate);              
        histamine += rate * kn1mastCellAllergy;
        antigenBal.AddStrain(RYEGRASSSTRAIN, -rate * kn2mastCellAllergy);
    } /* if */     

    rate = k2IgaProduction * plasmaCell.ReadValueWithProfile(INFLUENZASTRAIN,IGA) ;
    igaBal.AddStrain(INFLUENZASTRAIN, rate);                
    rate = k2IgeProduction * plasmaCell.ReadValueWithProfile(RYEGRASSSTRAIN,IGE) ;
    ige.AddStrain(RYEGRASSSTRAIN, rate);                

    rate = kGenerateGmcsf * macrophageApc.ReadTotal() ;
    bloodgmcsf += rate ;

    rate = kGenerateTnfAlpha * macrophageApc.ReadTotal() ;  
    tnfAlpha += rate ;
    rate = kHalfLifeTnfAlpha * tnfAlpha ;
    tnfAlpha -= rate;

    bloodbCellNaiveRecirculate.MigrateOutput(bCellNaiveRecirculate , inflammatoryRate * k2BloodInput_bCellNaiveRecirculate) ;
    bCellNaiveRecirculate.MigrateOutput(lymphOutputbCellNaiveRecirculate , k2LymphOutput_bCellNaiveRecirculate) ;
    bloodthEffector.MigrateOutputWithProfile(thEffector , inflammatoryRate * k2BloodInput_thEffector) ;
    bloodtcEffector.MigrateOutput(tcEffector , inflammatoryRate * k2BloodInput_tcEffector) ;
    bloodplasmaCell.MigrateOutputWithProfile(plasmaCell, inflammatoryRate * k2BloodInputPlasmaCell) ;

    bloodbCellMemory.MigrateOutputWithProfile(bCellMemory , inflammatoryRate * k2BloodInput_bCellMemory) ;
//    bloodthMemory.MigrateOutputWithProfile( thMemory, inflammatoryRate * k2BloodInput_thMemory) ;
  //  bloodtcMemory.MigrateOutputWithProfile( tcMemory, inflammatoryRate * k2BloodInput_tcMemory) ;
  bloodthMemory.MigrateOutputWithProfile( thMemory,  k2BloodInput_thMemory) ;
  bloodtcMemory.MigrateOutputWithProfile( tcMemory,  k2BloodInput_tcMemory) ;
    bCellMemory.MigrateOutputWithProfile(lymphOutputbCellMemory , inflammatoryOutputRate * k2LymphOutput_bCellMemory) ;
    thMemory.MigrateOutputWithProfile(lymphOutputthMemory , inflammatoryOutputRate * k2LymphOutput_thMemory) ;
    tcMemory.MigrateOutputWithProfile(lymphOutputtcMemory , inflammatoryOutputRate * k2LymphOutput_tcMemory) ;
                                                            
    rate = bloodmonocyte * inflammatoryMonocyteRate * k2BloodInput_Macrophage;
    bloodmonocyte -= rate ;
    macrophage += rate;
    rate = bloodmonocyte * inflammatoryMonocyteRate * k2BloodInput_Dendritic;
    bloodmonocyte -= rate ;
    dendriticImmature += rate;

    macrophageApc.MigrateOutput(lymphOutputmacrophageApc , k2LymphOutput_macrophageApc) ;
// dendriticApc.MigrateOutputWithProfile(lymphOutputdendriticApc , k2LymphOutput_dendriticApc) ;
    dendriticApc.MigrateOutputWithProfile(lymphOutputdendriticApc , inflammatoryDendriticOutputRate  * k2LymphOutput_dendriticApc) ;

    plasmaCell.MigrateOutput(kHalfLifePlasmaCell);
    macrophageApc.MigrateOutput(kHalfLifeMacrophageApc);

    rate = macrophage * k2MacrophageDie;
    macrophage -= rate;
    x1 = macrophage + macrophageApc.ReadTotal() - macrophageInitial ;   
    if (x1  <  0.0) {
        rate = macrophage  * k2macrophageReplicate;
        macrophage += rate;
    } /* if */     
    
    rate = k2DendriticDie * dendriticImmature; 
    dendriticImmature -= rate;
    x1 = dendriticImmature + dendriticApc.ReadTotal() - dendriticImmatureInitial ;
    if (x1  <  0.0) {
        rate = k2DendriticReplicate * dendriticImmature; 
        dendriticImmature += rate;
    } /* if */     
               
    rate = k2EffectorKill * macrophageApc.ReadValue(INFLUENZASTRAIN) * tcEffector.ReadValue(INFLUENZASTRAIN) ;  
    macrophageApc.AddStrain(INFLUENZASTRAIN,-rate) ;
    tcEffector.AddStrain(INFLUENZASTRAIN,-rate * knEffectorKill) ;

    rate = k2EffectorKillDendritic * dendriticApc.ReadValue(INFLUENZASTRAIN) * tcEffector.ReadValue(INFLUENZASTRAIN) ;  
    dendriticApc.AddStrain(INFLUENZASTRAIN,-rate) ;
    tcEffector.AddStrain(INFLUENZASTRAIN,-rate * knEffectorKill) ;

#if 0   /* disable for now?  */ 
    rate = k2EffectorKill * macrophageApc.ReadValue(RYEGRASSSTRAIN) * tcEffector.ReadValue(RYEGRASSSTRAIN) ;  
    macrophageApc.AddStrain(RYEGRASSSTRAIN,-rate) ;
    tcEffector.AddStrain(RYEGRASSSTRAIN,-rate * knEffectorKill) ;

    rate = k2EffectorKillDendritic * dendriticApc.ReadValue(RYEGRASSSTRAIN) * tcEffector.ReadValue(RYEGRASSSTRAIN) ;  
    dendriticApc.AddStrain(RYEGRASSSTRAIN,-rate) ;
    tcEffector.AddStrain(RYEGRASSSTRAIN,-rate * knEffectorKill) ;
#endif

    thMemory.ApcActivate(thMemoryBlast[0],dendriticApc,k2ThMemoryActivate,kmThMemoryActivate);
    thMemoryActivateCount += dthMemoryActivateCount;
    if (thMemoryActivateCount >= 1.0) {
        printf("********************** memory activation count 0:%g 1:%g 2:%g 3:%g  kthBlastActivateMemory:%g\n",thMemoryBlast[0].ReadValueWithProfile(RYEGRASSSTRAIN,TH2),thMemoryBlast[1].ReadValueWithProfile(RYEGRASSSTRAIN,TH2),thMemoryBlast[2].ReadValueWithProfile(RYEGRASSSTRAIN,TH2),thMemoryBlast[3].ReadValueWithProfile(RYEGRASSSTRAIN,TH2),kthBlastActivateMemory);
        thMemoryActivateCount = 0.0 ;
        for (i = (NUMBEROFTHMEMORYACTIVATE - 2); i >= 0; i--) {
            thMemoryBlast[i].MigrateOutputWithProfile(thMemoryBlast[i + 1], kthBlastActivateMemory) ; 
        } /* iForLoop */
    } /* if */                   
    thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ApcDeActivate(thMemory,dendriticApc, k2ThEffector2Memory,kmThEffector2Memory);
    x1 =  dendriticApc.ReadValue(RYEGRASSSTRAIN);
    x1 =  thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].ReadValueWithProfile(RYEGRASSSTRAIN,TH2) * x1;             
    rate = kGenerateIl3 * x1;
    il3 += rate ;             
    rate = kGenerateIl5 * x1;
    il5 += rate ;             
    rate = kHalfLifeil3 * il3 ;
    il3 -= rate;
    rate = kHalfLifeil5 * il5 ;
    il5 -= rate;          
    rate = kTransferil3 * il3 ;
    il3 -= rate;       
    bloodil3 += rate;       
    rate = kTransferil5 * il5 ;
    il5 -= rate;       
    bloodil5 += rate;                         
    thMemoryBlast[NUMBEROFTHMEMORYACTIVATE - 1].MigrateOutputWithProfile(lymphOutputthMemory , inflammatoryOutputRate * k2LymphOutput_thMemory) ;

    rate = kHalfLifehistamine * histamine ;
    histamine -= rate;
                 
    rate = k2mastCellNaive * mastCellNaive * ige.ReadValue(RYEGRASSSTRAIN) ;
    mastCellNaive -= rate ;                      
    mastCell.AddStrain(RYEGRASSSTRAIN, igeProfileGlobal ,rate);
    ige.AddStrain(RYEGRASSSTRAIN, -rate * knmastCellNaive);

    rate = kHalfLifemastCellNaive * mastCellNaive;
    mastCellNaive -= rate ;                      
  
    mastCellDegranulate.MigrateOutput(kHalfLifemastCellDegranulate);
    mastCell.MigrateOutput(kHalfLifemastCell);

    rate = bloodmastCell * il3inflammatoryRate * k2BloodInput_mastCell;
    bloodmastCell -= rate ;
    mastCellNaive += rate;

    rate = bloodeosinophil * il5inflammatoryRate * k2BloodInput_eosinophil ;
    bloodeosinophil -= rate ;
    eosinophil += rate;
                
 
    rate = k2eosinophilLtc4 * eosinophil * il5 * il5 * il5 * il5;
    //    rate = k2eosinophilLtc4 * eosinophil * il5 / (kmeosinophilLtc4 + il5);
    ltc4 += rate ;
    // printf("kmeosinophilLtc4:%g  k2eosinophilLtc4:%g  rate:%g il5:%g  x1:%g\n",kmeosinophilLtc4,k2eosinophilLtc4,rate,il5,x1);
    
    rate = kHalfLifeltc4 * ltc4 ;
    ltc4 -= rate;

    rate = kHalfLifeeosinophil * eosinophil;
    eosinophil -= rate ;                      

    x1 = histamine + (kltc4multiplier * ltc4) ;
    fev1 = 100.0 * (1.0 - k2fev1 * x1 / (kmfev1 + x1));
}
                       

                       
void  GenericImmuneTissue::ExecuteLaminaProperia ()
{
    double  rate,x1;
    
    /* bal equations */
    antigenBal.MigrateOutput(k2MucociliaryClearance);

    rate = antigenBal.ReadValue(INFLUENZASTRAIN);
    if (rate > 1.0e-10) {        /* hack, when antigen is essentially gone, don't evaluate  */ 
        rate *= k2InfluenzaNeutralize * igaBal.ReadValue(INFLUENZASTRAIN);
        antigenBal.AddStrain(INFLUENZASTRAIN, -rate);
        igaBal.AddStrain(INFLUENZASTRAIN, -rate * knInfluenzaNeutralize);
    } /* if */     

    igaBal.MigrateOutput(kHalfLifeIgA);

    /* Epithelia equations */
    rate = k2EpitheliaReplication  * epitheliaDead;
    epitheliaDead -= rate;
    epitheliaCell += rate;      /* replication/fibroblasts */

    rate = k2EpitheliaInfection * epitheliaCell * antigenBal.ReadValue(INFLUENZASTRAIN) ;
    epitheliaCell -= rate ;
    epitheliaApc += rate ;
    antigenBal.AddStrain(INFLUENZASTRAIN, -rate * knEpitheliaInfection);

    rate = k2EpitheliaResistive * epitheliaCell * interferonAlpha ;
    epitheliaResistive += rate ;
    epitheliaCell -= rate ;
    interferonAlpha -= rate * knEpitheliaResistive;

    rate = k2EpitheliaDie * epitheliaCell ;
    epitheliaCell -= rate ;
    epitheliaDead += rate;

    rate = k2EpitheliaResistiveDie * epitheliaResistive ;
    epitheliaResistive -= rate ;
    epitheliaCell += rate;

    rate = k2VirusReplication * epitheliaApc ;
    antigenBal.AddStrain(INFLUENZASTRAIN, rate);
    rate = k2EpitheliaApcDie * epitheliaApc ;
    epitheliaApc -= rate ;
    epitheliaDead += rate;

    rate = k2EffectorKill * epitheliaApc * tcEffector.ReadValue(INFLUENZASTRAIN) ;
    epitheliaApc -= rate ;
    epitheliaDead += rate;
    tcEffector.AddStrain(INFLUENZASTRAIN, -rate * knEffectorKill);

    tcEffector.MigrateAicd(dendriticApc, k2tcAicd,kmtcAicd,k0tcAicd); 
    thEffector.MigrateAicd(dendriticApc, k2thAicd,kmthAicd,k0thAicd); 
    tcEffector.ApcDeActivate(tcMemory,dendriticApc, k2TcEffector2Memory,kmTcEffector2Memory);
    thEffector.ApcDeActivate(thMemory,dendriticApc, k2ThEffector2Memory,kmThEffector2Memory);

    rate = k2MacrophageInfection * macrophage * antigenBal.ReadValue(INFLUENZASTRAIN) ;
    macrophage -= rate ;
    macrophageApc.AddStrain(INFLUENZASTRAIN, rate);
    antigenBal.AddStrain(INFLUENZASTRAIN, -rate * knMacrophageInfection);

    rate = k2GenerateInterferonAlpha * macrophageApc.ReadTotal() ;
    interferonAlpha += rate;                  

    rate = interferonAlpha * kHalfLifeInterferonAlpha;
    interferonAlpha -= rate;

    /* Interstitium equations */                                            
    inflammatoryRate = 1.0 + knInflammatory * tnfAlpha / (kmInflammatory + tnfAlpha);
    inflammatoryMonocyteRate = 1.0 + knMonocyteInflammatory * tnfAlpha / (kmInflammatory + tnfAlpha);
    inflammatoryOutputRate = 1.0 + knInflammatoryOutput * tnfAlpha / (kmInflammatoryOutput + tnfAlpha);
    inflammatoryDendriticOutputRate = 1.0 + knInflammatoryDendriticOutput * tnfAlpha / (kmInflammatoryOutput + tnfAlpha);
    
    rate = k2DendriticInfection * dendriticImmature * antigenBal.ReadValue(INFLUENZASTRAIN) ;
    dendriticImmature -= rate ;
    dendriticApc.AddStrain(INFLUENZASTRAIN, kDendriticInfectionProfile, rate);
    antigenBal.AddStrain(INFLUENZASTRAIN, -rate * knDendriticInfection);


    rate = k2IgaProduction * plasmaCell.ReadValueWithProfile(INFLUENZASTRAIN,IGA) ;
    igaBal.AddStrain(INFLUENZASTRAIN, rate);                

    rate = kGenerateGmcsf * macrophageApc.ReadTotal() ;
    bloodgmcsf += rate ;

    rate = kGenerateTnfAlpha * macrophageApc.ReadTotal() ;  
    tnfAlpha += rate ;
    rate = kHalfLifeTnfAlpha * tnfAlpha ;
    tnfAlpha -= rate;

    bloodbCellNaiveRecirculate.MigrateOutput(bCellNaiveRecirculate , inflammatoryRate * k2BloodInput_bCellNaiveRecirculate) ;
    bCellNaiveRecirculate.MigrateOutput(lymphOutputbCellNaiveRecirculate , k2LymphOutput_bCellNaiveRecirculate) ;
    bloodthEffector.MigrateOutputWithProfile(thEffector , inflammatoryRate * k2BloodInput_thEffector) ;
    bloodtcEffector.MigrateOutput(tcEffector , inflammatoryRate * k2BloodInput_tcEffector) ;
    bloodplasmaCell.MigrateOutputWithProfile(plasmaCell, inflammatoryRate * k2BloodInputPlasmaCell) ;

    bloodbCellMemory.MigrateOutputWithProfile(bCellMemory , inflammatoryRate * k2BloodInput_bCellMemory) ;
//    bloodthMemory.MigrateOutputWithProfile( thMemory, inflammatoryRate * k2BloodInput_thMemory) ;
  //  bloodtcMemory.MigrateOutputWithProfile( tcMemory, inflammatoryRate * k2BloodInput_tcMemory) ;
  bloodthMemory.MigrateOutputWithProfile( thMemory,  k2BloodInput_thMemory) ;
  bloodtcMemory.MigrateOutputWithProfile( tcMemory,  k2BloodInput_tcMemory) ;
    bCellMemory.MigrateOutputWithProfile(lymphOutputbCellMemory , inflammatoryOutputRate * k2LymphOutput_bCellMemory) ;
    thMemory.MigrateOutputWithProfile(lymphOutputthMemory , inflammatoryOutputRate * k2LymphOutput_thMemory) ;
    tcMemory.MigrateOutputWithProfile(lymphOutputtcMemory , inflammatoryOutputRate * k2LymphOutput_tcMemory) ;
                                                            
    rate = bloodmonocyte * inflammatoryMonocyteRate * k2BloodInput_Macrophage;
    bloodmonocyte -= rate ;
    macrophage += rate;
    rate = bloodmonocyte * inflammatoryMonocyteRate * k2BloodInput_Dendritic;
    bloodmonocyte -= rate ;
    dendriticImmature += rate;

    macrophageApc.MigrateOutput(lymphOutputmacrophageApc , k2LymphOutput_macrophageApc) ;
// dendriticApc.MigrateOutputWithProfile(lymphOutputdendriticApc , k2LymphOutput_dendriticApc) ;
    dendriticApc.MigrateOutputWithProfile(lymphOutputdendriticApc , inflammatoryDendriticOutputRate  * k2LymphOutput_dendriticApc) ;

    plasmaCell.MigrateOutput(kHalfLifePlasmaCell);
    macrophageApc.MigrateOutput(kHalfLifeMacrophageApc);

    rate = macrophage * k2MacrophageDie;
    macrophage -= rate;
    x1 = macrophage + macrophageApc.ReadTotal() - macrophageInitial ;   
    if (x1  <  0.0) {
        rate = macrophage  * k2macrophageReplicate;
        macrophage += rate;
    } /* if */     
    
    rate = k2DendriticDie * dendriticImmature; 
    dendriticImmature -= rate;
    x1 = dendriticImmature + dendriticApc.ReadTotal() - dendriticImmatureInitial ;
    if (x1  <  0.0) {
        rate = k2DendriticReplicate * dendriticImmature; 
        dendriticImmature += rate;
    } /* if */     
               
    rate = k2EffectorKill * macrophageApc.ReadValue(INFLUENZASTRAIN) * tcEffector.ReadValue(INFLUENZASTRAIN) ;  
//    macrophageApc.AddStrain(INFLUENZASTRAIN,-rate) ;
  //  tcEffector.AddStrain(INFLUENZASTRAIN,-rate * knEffectorKill) ;

    rate = k2EffectorKillDendritic * dendriticApc.ReadValue(INFLUENZASTRAIN) * tcEffector.ReadValue(INFLUENZASTRAIN) ;  
    dendriticApc.AddStrain(INFLUENZASTRAIN,-rate) ;
    tcEffector.AddStrain(INFLUENZASTRAIN,-rate * knEffectorKill) ;
}