/// <summary>
/// Update cell (metabolize and update diffusion of particles)
/// </summary>
public void Update(double updateInterval, Habitat hab)
{
//diffusion
foreach (Particle cellParticle in particles)
{
foreach (Particle habParticle in hab.Particles)
{
if (cellParticle.ChemicalSpecies == habParticle.ChemicalSpecies)
{
double flowIntoCell = updateInterval * surfaceArea * ((cellParticle.ConcentrationConstant * (habParticle.Concentration - cellParticle.Concentration)) + (cellParticle.TemperatureConstant * (hab.Temperature - temperature)));
cellParticle.Quantity += flowIntoCell;
cellParticle.UpdateConcentration(this.volume);
habParticle.Quantity -= flowIntoCell;
habParticle.UpdateConcentration(hab.Volume);
}
}
}
//enzymatic activity
foreach (Particle substrate in this.particles)
{
foreach (Enzyme enzyme in this.enzymes)
{
//check if this enzyme acts on this partile as a substrate
if (enzyme.SubstrateSpecies == substrate.ChemicalSpecies)
{
enzyme.UpdateConcentration(this.volume);
enzyme.UpdateComplexConcentration(substrate.Concentration);
foreach (Particle potentialProduct in particles)
{
if (potentialProduct.ChemicalSpecies == enzyme.ProductSpecies)
{
//update product's quantity based on derivative
potentialProduct.Quantity += this.volume *
Particle.CalculateReactionDerivative(enzyme.MaximumReactionRate, enzyme.DissociationConstant, substrate.Concentration) * updateInterval;
//update substrate's quantity based on derivative
substrate.Quantity += this.volume *
(-enzyme.FrwrdRate * enzyme.Concentration * substrate.Concentration
+ enzyme.RvrsRate * enzyme.ComplexConcentration) * updateInterval;
//update substrate's concentration
substrate.UpdateConcentration(this.volume);
//update enzyme's quantity based on derivative
enzyme.Quantity += this.volume *
(-enzyme.FrwrdRate * enzyme.Concentration * substrate.Concentration
+ enzyme.RvrsRate * enzyme.ComplexConcentration +
enzyme.CatRate * enzyme.ComplexConcentration) * updateInterval;
}
}
}
}
}
//Update records of states
foreach (Particle particle in this.particles)
{
particle.UpdateRecords();
}
foreach (Enzyme enzyme in this.enzymes)
{
enzyme.UpdateRecords();
}
}
static void Main(string[] args)
{
//Tests
//Constants
//in cubic meters
double cellVolume = .000001;
double habVolume = 1;
double sub1ConcentrationConstant = 500;
double sub1TemperatureConstant = 350;
//in moles
double sub1CellInitQuantity = .0015;
double sub2ConcentrationConstant = 150;
double sub2TemperatureConstant = 30;
//in moles
double sub2CellInitQuantity = .0008;
double prod1ConcentrationConstant = 300;
double prod1TemperatureConstant = 180;
//in moles
double prod1CellInitQuantity = 0;
double prod2ConcentrationConstant = 380;
double prod2TemperatureConstant = 65;
//in moles
double prod2CellInitQuantity = 0;
double enz1FrwrdRate = 16000;
double enz1RvrsRate = 950;
double enz1CatRate = 9700;
//in moles
double enz1InitQuantity = .00000175;
double enz2FrwrdRate = 920;
double enz2RvrsRate = 105;
double enz2CatRate = 6400;
//in moles
double enz2InitQuantity = .00000257;
//Initiating particle/enzyme lists for the cell and its habitat
List <Particle> cellParts = new List <Particle>();
List <Particle> habParts = new List <Particle>();
List <Enzyme> cellEnzs = new List <Enzyme>();
List <Enzyme> habEnzs = new List <Enzyme>();
//Creating the particle structures
Particle sub1Cell = new Particle(ChemicalSpecies.Substrate1, sub1ConcentrationConstant, sub1TemperatureConstant,
sub1CellInitQuantity, cellVolume);
Particle sub2Cell = new Particle(ChemicalSpecies.Substrate2, sub2ConcentrationConstant, sub2TemperatureConstant,
sub2CellInitQuantity, cellVolume);
Particle sub1Hab = new Particle(ChemicalSpecies.Substrate1, sub1ConcentrationConstant, sub1TemperatureConstant,
sub1CellInitQuantity, cellVolume);
Particle sub2Hab = new Particle(ChemicalSpecies.Substrate2, sub2ConcentrationConstant, sub2TemperatureConstant,
sub2CellInitQuantity, cellVolume);
Particle prod1Cell = new Particle(ChemicalSpecies.Product1, prod1ConcentrationConstant, prod1TemperatureConstant,
prod1CellInitQuantity, cellVolume);
Particle prod2Cell = new Particle(ChemicalSpecies.Product2, prod2ConcentrationConstant, prod2TemperatureConstant,
prod2CellInitQuantity, cellVolume);
Particle prod1Hab = new Particle(ChemicalSpecies.Product1, prod1ConcentrationConstant, prod1TemperatureConstant,
prod1CellInitQuantity, habVolume);
Particle prod2Hab = new Particle(ChemicalSpecies.Product2, prod2ConcentrationConstant, prod2TemperatureConstant,
prod2CellInitQuantity, habVolume);
//Creating the enzyme structures
Enzyme enzyme1 = new Enzyme(ChemicalSpecies.Substrate1, ChemicalSpecies.Product1, enz1FrwrdRate, enz1RvrsRate,
enz1CatRate, enz1InitQuantity, cellVolume);
Enzyme enzyme2 = new Enzyme(ChemicalSpecies.Substrate2, ChemicalSpecies.Product2, enz2FrwrdRate, enz2RvrsRate,
enz2CatRate, enz2InitQuantity, cellVolume);
//Creating Particle and Enzyme Lists
cellParts.Add(sub1Cell);
cellParts.Add(sub2Cell);
cellParts.Add(prod1Cell);
cellParts.Add(prod2Cell);
cellEnzs.Add(enzyme1);
cellEnzs.Add(enzyme2);
habParts.Add(sub1Hab);
habParts.Add(sub2Hab);
habParts.Add(prod1Hab);
habParts.Add(prod2Hab);
//Creating the cell and its "habitat"
Cell VC = new Cell(cellParts, cellEnzs, cellVolume, 27);
List <Cell> habCells = new List <Cell>();
habCells.Add(VC);
Habitat hab = new Habitat(habParts, habCells, 27, habVolume);
//Run simulation/"live"/update
hab.WriteCurrentState();
hab.Update(20, 1);
hab.WriteCurrentState();
Console.ReadKey();
}
