InitalCommit

BaseCellSimulation/Enzyms/Lysosome/Cathepsin.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Lysosome
+{
+    public class Cathepsin : InternalEnzym
+    {
+        public Cathepsin()
+        {
+            Vmax = 0.2; // mM/s, empirisch
+            Km = 0.1;   // mM
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Protein.Waste);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double degraded = rate * dt;
+            degraded = Math.Min(degraded, res.Res.Protein.Waste);
+
+            res.Res.Protein.Waste -= degraded;
+            res.Res.Protein.AminoAcids += degraded * 0.5; // 50% verwertbar
+            res.Res.Energy.ATP += degraded * 0.05;        // kleine ATP-Rückgewinnung
+            res.Res.Energy.NADH += degraded * 0.01;       // minimale Redoxreaktion
+        }
+    }
+
+}

BaseCellSimulation/Enzyms/Lysosome/GenericLysosomalEnzyme.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Lysosome
+{
+    public class GenericLysosomalEnzyme : InternalEnzym
+    {
+        public GenericLysosomalEnzyme()
+        {
+            Vmax = 0.2;
+            Km = 0.1;
+        }
+
+        double redoxRatio = 0.0;
+
+        public override void ComputeRate(Resources res)
+        {
+            // --- Grundrate basierend auf Protein-Waste ---
+            rate = Michaelis_Menten(res.Protein.Waste, Vmax, Km);
+
+            // --- Energieabhängigkeit ---
+            double energyCharge = (res.Energy.ATP + 0.5 * res.Energy.ADP) /
+                                  (res.Energy.ATP + res.Energy.ADP + res.Energy.AMP + 1e-9);
+            rate *= Math.Clamp(energyCharge, 0.0, 1.0);
+
+            // --- Redoxabhängigkeit ---
+            redoxRatio = res.Energy.NAD / (res.Energy.NAD + res.Energy.NADH + 1e-9);
+            rate *= Math.Clamp(redoxRatio, 0.0, 1.0);
+
+            // --- pH-Abhängigkeit ---
+            double acidFactor = 1.0 - 0.5 * Math.Clamp(res.Ions.Protons / 1.0, 0.0, 1.0);
+            rate *= acidFactor;
+
+            // --- Stressfaktor bei hohen ROS ---
+            double stressPenalty = res.Ions.ROS > 1.0 ? 0.5 : 1.0;
+            rate *= stressPenalty;
+        }
+
+        public override void ApplyChanges(CellRessources Resources, double dt)
+        {
+            var res = Resources.Res;
+            var ca = Resources.Res.Ca;
+
+            ComputeRate(res);
+
+            double degraded = Math.Min(res.Protein.Waste, rate * dt);
+            if (degraded <= 0.0)
+                return;
+
+            // --- Protein-Abbau ---
+            res.Protein.Waste -= degraded;
+
+            // --- Energieverbrauch & minimale Rückgewinnung ---
+            double atpUsed = degraded * 0.15;
+            double atpRecovered = degraded * 0.03 * ((res.Energy.ATP + 0.5 * res.Energy.ADP) /
+                                                    (res.Energy.ATP + res.Energy.ADP + res.Energy.AMP + 1e-9));
+            Resources.ConsumeATP(atpUsed);
+            res.Energy.ATP += atpRecovered;
+
+            // --- NAD+ → NADH Redoxreaktion ---
+            double nadUsed = degraded * 0.08;
+            double actualNadUsed = Math.Min(nadUsed, res.Energy.NAD);
+            res.Energy.NAD -= actualNadUsed;
+            res.Energy.NADH += actualNadUsed;
+
+            // --- Aminosäuren-Recycling ---
+            double recyclingEfficiency = 0.4 + 0.3 * ((res.Energy.ATP + 0.5 * res.Energy.ADP) /
+                                                     (res.Energy.ATP + res.Energy.ADP + res.Energy.AMP + 1e-9));
+            res.Protein.AminoAcids += degraded * recyclingEfficiency;
+
+            // --- Sekundäre Effekte: ROS, Heat, Protonen ---
+            res.Ions.ROS += degraded * (1.0 - redoxRatio) * 0.01;
+            res.Heat += degraded * 0.05;
+            res.Ions.Protons += degraded * 0.005;
+
+            // --- Kalziumleckage als Stresssignal ---
+            ca.CytosolicCa += degraded * 0.00002;
+
+            // --- Lysosomenaktivität für Feedback ---
+            ca.LysosomeActivity = Math.Clamp(rate / Vmax, 0.0, 1.0);
+        }
+    }
+
+
+}

BaseCellSimulation/Enzyms/Lysosome/LysosomalLipase.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Lysosome
+{
+    public class LysosomalLipase : InternalEnzym
+    {
+        public LysosomalLipase()
+        {
+            Vmax = 0.1;
+            Km = 0.05;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Lipids); // falls Lipide modelliert werden
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double degraded = rate * dt;
+            degraded = Math.Min(degraded, res.Res.Lipids);
+
+            res.Res.Lipids -= degraded;
+            res.Res.Energy.ATP += degraded * 0.02; // minimaler ATP Gewinn
+        }
+    }
+}

BaseCellSimulation/Enzyms/Lysosome/LysosomalNuclease.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Lysosome
+{
+    public class LysosomalNuclease : InternalEnzym
+    {
+        public LysosomalNuclease()
+        {
+            Vmax = 0.15;
+            Km = 0.05;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Protein.NucleicAcids); // falls RNA/DNA modelliert
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double degraded = rate * dt;
+            degraded = Math.Min(degraded, res.Res.Protein.NucleicAcids);
+
+            res.Res.Protein.NucleicAcids -= degraded;
+            res.Res.Protein.Nucleotides += degraded; // freiwerdende Nucleotide
+            res.Res.Energy.ATP += degraded * 0.01;
+        }
+    }
+}

BaseCellSimulation/Enzyms/Lysosome/LysosomalPhosphatase.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Lysosome
+{
+    public class LysosomalPhosphatase : InternalEnzym
+    {
+        public LysosomalPhosphatase()
+        {
+            Vmax = 0.1;
+            Km = 0.05;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.PhosphorylatedSubstrates);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double degraded = rate * dt;
+            degraded = Math.Min(degraded, res.Res.PhosphorylatedSubstrates);
+
+            res.Res.PhosphorylatedSubstrates -= degraded;
+            res.Res.Phosphate.Pi += degraded;
+            res.Res.Phosphate.PPi += degraded * 0.1; // falls Pyrophosphat entsteht
+        }
+    }
+}