public void AssertStability(SimulationParameters simulationParameters, BaseBiosensor biosensor)
{
var isReactionStable = GetReactionStability(biosensor.VMax, biosensor.Km, simulationParameters.t);
if (!isReactionStable)
{
throw new Exception("Simulation scheme is not stable");
}
foreach (var layer in biosensor.Layers)
{
if (layer.N == 0 || layer.Type == LayerType.SelectiveMembrane)
{
continue;
}
var Dmax = Math.Max(layer.Substrate.DiffusionCoefficient, layer.Product.DiffusionCoefficient);
var isLayerStable = GetDiffusionStability(Dmax, layer.H, simulationParameters.t);
if (!isLayerStable)
{
throw new Exception("Simulation scheme is not stable");
}
}
}
public double GetZeroOrderAnalyticalSolutionForTwoLayerModel(BaseBiosensor biosensor, SimulationParameters simulationParameters)
{
var S0 = biosensor.S0;
var enzymeLayer = biosensor.EnzymeLayer;
var diffusionLayer = biosensor.DiffusionLayer;
var alpha = Math.Sqrt(biosensor.VMax * enzymeLayer.Height * enzymeLayer.Height
/ (biosensor.Km * enzymeLayer.Substrate.DiffusionCoefficient));
var firstMultiplier = simulationParameters.ne * simulationParameters.F *
enzymeLayer.Product.DiffusionCoefficient *
S0 / (enzymeLayer.Height + diffusionLayer.Height);
var secondMultiplier = enzymeLayer.Height + diffusionLayer.Height *
(diffusionLayer.Substrate.DiffusionCoefficient - alpha *
enzymeLayer.Substrate.DiffusionCoefficient * Math.Sinh(alpha) / Math.Cosh(alpha)) /
(diffusionLayer.Substrate.DiffusionCoefficient + alpha *
(diffusionLayer.Height / enzymeLayer.Height) *
enzymeLayer.Substrate.DiffusionCoefficient * Math.Sinh(alpha) / Math.Cosh(alpha));
var thirdMultiplier =
alpha * enzymeLayer.Substrate.DiffusionCoefficient * diffusionLayer.Height * Math.Sinh(alpha) /
(enzymeLayer.Height * Math.Cosh(alpha)) + enzymeLayer.Substrate.DiffusionCoefficient *
diffusionLayer.Product.DiffusionCoefficient /
enzymeLayer.Product.DiffusionCoefficient *
(1 - 1 / Math.Cosh(alpha));
return(firstMultiplier * secondMultiplier * thirdMultiplier / (diffusionLayer.Product.DiffusionCoefficient *
enzymeLayer.Height + enzymeLayer.Product.DiffusionCoefficient * diffusionLayer.Height));
}
private static double GetZeroOrderAnalyticalSolutionForSingleLayerModel(BaseBiosensor biosensor, SimulationParameters simulationParameters)
{
var enzymeLayer = biosensor.EnzymeLayer;
var iCur = simulationParameters.ne * simulationParameters.F * biosensor.VMax * enzymeLayer.Height / 2;
return(iCur);
}
protected BaseSimulation(
SimulationParameters simulationParameters,
BaseBiosensor biosensor,
IResultPrinter resultPrinter)
{
SimulationParameters = simulationParameters;
Biosensor = biosensor;
ResultPrinter = resultPrinter;
}
public ImplicitSchemeParameters(BaseBiosensor biosensor, Layer layer, Substance substance)
{
var a = substance.DiffusionCoefficient * layer.R;
var c = 1 + 2 * a;
var n = layer.N;
A = new double[n];
B = new double[n];
C = new double[n];
D = new double[n];
E = new double[n];
F = new double[n];
for (var i = 1; i < n - 1; i++)
{
A[i] = B[i] = a;
C[i] = c;
}
if (substance is Substrate)
{
A[0] = 0;
C[0] = 1;
B[n - 1] = 0;
C[n - 1] = 1;
Niu1 = 0;
Niu2 = biosensor.S0;
Beta1 = 1;
Beta2 = 0;
}
if (substance is Product)
{
A[0] = 0;
C[0] = 1;
B[n - 1] = 0;
C[n - 1] = 1;
Niu1 = 0;
Niu2 = 0;
Beta1 = 0;
Beta2 = 0;
}
A[n - 1] = Beta2;
B[0] = Beta1;
U0 = U1 = 0;
Y0 = Y1 = 0;
}
private static double GetFirstOrderAnalyticSolutionForTwoLayerModel(BaseBiosensor biosensor, SimulationParameters simulationParameters)
{
var enzymeLayer = biosensor.EnzymeLayer;
var diffusionLayer = biosensor.DiffusionLayer;
var iCur = simulationParameters.ne * simulationParameters.F * biosensor.VMax * enzymeLayer.Height *
(diffusionLayer.Product.DiffusionCoefficient * diffusionLayer.Height +
2 * enzymeLayer.Product.DiffusionCoefficient * diffusionLayer.Height) /
(2 * (diffusionLayer.Product.DiffusionCoefficient * diffusionLayer.Height +
enzymeLayer.Product.DiffusionCoefficient * diffusionLayer.Height));
return(iCur);
}
private static double GetFirstOrderAnalyticSolutionForSingleLayerModel(BaseBiosensor biosensor, SimulationParameters simulationParameters)
{
var S0 = 0.01 * biosensor.Km;
var enzymeLayer = biosensor.EnzymeLayer;
var alpha = Math.Sqrt(biosensor.VMax / (biosensor.Km * enzymeLayer.Substrate.DiffusionCoefficient));
var iCur = simulationParameters.ne * simulationParameters.F * enzymeLayer.Product.DiffusionCoefficient *
S0 / enzymeLayer.Height * (1 - 1 / Math.Cosh(alpha * enzymeLayer.Height));
return(iCur);
}
public double GetFirstOrderAnalyticSolution(BaseBiosensor biosensor, SimulationParameters simulationParameters)
{
if (biosensor.Layers.Count == 1)
{
return(GetFirstOrderAnalyticSolutionForSingleLayerModel(biosensor, simulationParameters));
}
if (biosensor.Layers.Count == 2)
{
return(GetFirstOrderAnalyticSolutionForTwoLayerModel(biosensor, simulationParameters));
}
return(0);
}
public ExplicitSchemeCalculator(BaseBiosensor biosensor, SimulationParameters simulationParameters)
{
Biosensor = biosensor;
SimulationParameters = simulationParameters;
foreach (var layer in biosensor.Layers)
{
layer.Product.ExplicitScheme = new ExplicitSchemeParameters(layer, layer.Product);
if (layer.Type == LayerType.SelectiveMembrane)
{
continue;
}
layer.Substrate.ExplicitScheme = new ExplicitSchemeParameters(layer, layer.Substrate);
}
}
public SimulationParametersSuplier1(BaseBiosensor biosensor)
{
ne = 2;
DecayRate = 1e-4;
F = 96485.33289;
ZeroIBond = 1e-25;
t = 7.5e-6;
LayersSteps = new List <KeyValuePair <LayerType, long> >
{
new KeyValuePair <LayerType, long>(LayerType.SelectiveMembrane, 100),
new KeyValuePair <LayerType, long>(LayerType.PerforatedMembrane, 100),
new KeyValuePair <LayerType, long>(LayerType.DiffusionLayer, 100),
new KeyValuePair <LayerType, long>(LayerType.Enzyme, 100)
};
long lastLayerMaxIndex = 0;
foreach (var layer in biosensor.Layers)
{
layer.N = GetLayerSteps(layer.Type);
N += layer.N;
layer.LowerBondIndex = lastLayerMaxIndex;
if (lastLayerMaxIndex == 0)
{
lastLayerMaxIndex--;
}
lastLayerMaxIndex = layer.UpperBondIndex = lastLayerMaxIndex + layer.N;
if (layer.N == 0)
{
continue;
}
layer.H = layer.Height / layer.N;
layer.R = t / (layer.H * layer.H);
}
}
public CylindricMicroreactors1D(
SimulationParameters simulationParameters,
BaseBiosensor biosensor,
IResultPrinter resultPrinter) : base(simulationParameters, biosensor, resultPrinter)
{
}
public SingleLayerSimulation1D(
SimulationParameters simulationParameters,
BaseBiosensor biosensor,
IResultPrinter resultPrinter) : base(simulationParameters, biosensor, resultPrinter)
{
}
public PerforatedMembrane1D(
SimulationParameters simulationParameters,
BaseBiosensor biosensor,
IResultPrinter resultPrinter) : base(simulationParameters, biosensor, resultPrinter)
{
}
public CrankNicolsonScheme(BaseBiosensor biosensor, SimulationParameters simulationParameters)
{
Biosensor = biosensor;
SimulationParameters = simulationParameters;
}
