InitalCommit

BaseCellSimulation/Enzyms/Nucleus/DNA_Polymerase_Delta.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Nucleus
+{
+    public class DNA_Polymerase_Delta : InternalEnzym
+    {
+        private const double EnergyCostATP = 0.5;
+
+        public DNA_Polymerase_Delta()
+        {
+            Km = 0.05;
+            Vmax = 1.2;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double dDna = Math.Min(rate * dt, res.Res.Protein.dNTP);
+            dDna = res.Res.Energy.ATP >= dDna * EnergyCostATP ? dDna : res.Res.Energy.ATP / EnergyCostATP;
+            res.Res.Protein.dNTP -= dDna;
+            res.Res.Nucleus.ReplicationProgress += dDna;
+            res.ConsumeATP(dDna * EnergyCostATP);
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Protein.dNTP);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Nucleus/DNMT1.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Nucleus
+{
+    public class DNMT1 : InternalEnzym
+    {
+        public DNMT1()
+        {
+            Km = 0.01;
+            Vmax = 0.25;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            // Berechne tatsächlich übertragene Methylmenge
+            double dMethyl = Math.Min(rate * dt, res.Res.Protein.SAM);
+
+            // Chromatinzugänglichkeit moduliert Effektivität
+            double accessibilityFactor = Math.Clamp(res.Res.Nucleus.ChromatinAccessibility / 0.005, 0.1, 1.0);
+            dMethyl *= accessibilityFactor;
+
+            // SAM → SAH Umwandlung
+            res.Res.Protein.SAM -= dMethyl;
+            res.Res.Protein.SAH += dMethyl;  // 1:1 Bildung
+
+            // Methylierung der DNA (vereinfachte Darstellung)
+            res.Res.Nucleus.ChromatinAccessibility -= dMethyl * 0.005;
+            if (res.Res.Nucleus.ChromatinAccessibility < 0)
+                res.Res.Nucleus.ChromatinAccessibility = 0;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            double activityFactor = Math.Min(1.0, res.Nucleus.ReplicationProgress / 10.0);
+            Michaelis_Menten(res.Protein.SAM * activityFactor);
+            rate *= activityFactor;
+        }
+    }
+}

BaseCellSimulation/Enzyms/Nucleus/HistoneAcetyltransferase.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Nucleus
+{
+    public class HistoneAcetyltransferase : InternalEnzym
+    {
+        public HistoneAcetyltransferase()
+        {
+            Km = 0.01;
+            Vmax = 0.3;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double dA = Math.Min(rate * dt, res.Res.Protein.AcetylCoA);
+            res.Res.Protein.AcetylCoA -= dA;
+            res.Res.Nucleus.ChromatinAccessibility = Math.Min(1.0, res.Res.Nucleus.ChromatinAccessibility + dA * 0.1);
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Protein.AcetylCoA);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Nucleus/HistoneDeacetylase.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Nucleus
+{
+    public class HistoneDeacetylase : InternalEnzym
+    {
+        public HistoneDeacetylase()
+        {
+            Km = 0.02;
+            Vmax = 0.25;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double dD = Math.Min(rate * dt, Math.Min(res.Res.Nucleus.ChromatinAccessibility / 0.1, res.Res.Energy.NAD));
+            res.Res.Energy.NAD -= dD;
+            res.Res.Energy.NADH += dD * 0.5;
+            res.Res.Nucleus.ChromatinAccessibility = Math.Max(0.0, res.Res.Nucleus.ChromatinAccessibility - dD * 0.1);
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Energy.NAD);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Nucleus/PARP1.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Nucleus
+{
+    public class PARP1 : InternalEnzym
+    {
+        private const double EnergyCostATP = 0.3;
+
+        public PARP1()
+        {
+            Km = 0.02;
+            Vmax = 0.4;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double dRepair = Math.Min(rate * dt, res.Res.Protein.DNA_damage);
+            dRepair = res.Res.Energy.NAD >= dRepair * EnergyCostATP ? dRepair : res.Res.Energy.NAD / EnergyCostATP;
+            res.Res.Energy.NAD -= dRepair * EnergyCostATP;
+            res.Res.Energy.NADH += dRepair * 0.2;
+            res.Res.Protein.DNA_damage -= dRepair * 0.8; 
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Protein.DNA_damage);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Nucleus/RNA_Polymerase_II.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Nucleus
+{
+    public class RNA_Polymerase_II : InternalEnzym
+    {
+        private const double EnergyCostATP = 0.3;
+
+        public RNA_Polymerase_II()
+        {
+            Km = 0.02;
+            Vmax = 0.8;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double dM = Math.Min(rate * dt, res.Res.Protein.NTP);
+            dM = res.Res.Energy.ATP >= dM * EnergyCostATP ? dM : res.Res.Energy.ATP / EnergyCostATP;
+            res.Res.Protein.NTP -= dM;
+            res.Res.Protein.mRNA += dM;
+            res.ConsumeATP(dM * EnergyCostATP);
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Protein.NTP);
+            rate *= res.Nucleus.ChromatinAccessibility;
+        }
+    }
+}

BaseCellSimulation/Enzyms/Nucleus/Topoisomerase_II.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Nucleus
+{
+    public class Topoisomerase_II : InternalEnzym
+    {
+        private const double EnergyCostATP = 0.2;
+
+        public Topoisomerase_II()
+        {
+            Km = 0.03;
+            Vmax = 0.5;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double repair = Math.Min(rate * dt, res.Res.Protein.DNA_damage);
+            repair = res.Res.Energy.ATP >= repair * EnergyCostATP ? repair : res.Res.Energy.ATP / EnergyCostATP;
+            res.Res.Protein.DNA_damage -= repair;
+            res.ConsumeATP(repair * EnergyCostATP);
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Protein.DNA_damage);
+        }
+    }
+}