InitalCommit

BaseCellSimulation/BaseCellSimulation.csproj

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+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <TargetFramework>net9.0</TargetFramework>
+    <ImplicitUsings>enable</ImplicitUsings>
+    <Nullable>enable</Nullable>
+  </PropertyGroup>
+
+</Project>

BaseCellSimulation/Cell.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation
+{
+    public struct cellInfo
+    {
+        public double time;
+        public CellState state;
+        public Dictionary<string, double> resources;
+        public CellCaState caState;
+        public override string ToString()
+        {
+            StringBuilder sb = new();
+            sb.AppendLine($"Time: {time}, State: {state}");
+            foreach (var kvp in resources)
+            {
+                sb.AppendLine($"{kvp.Key}: {kvp.Value}");
+            }
+            return sb.ToString();
+        }
+    }
+
+    public class Cell
+    {
+        private List<Organell> organelles = new();
+        private CellRessources resources;
+        private CellState state = CellState.Resting;
+        private double time = 0.0;
+        private Random rng = new();
+        private CellCaState caState = new();
+
+        public EnviromentState EnviromentState { get { return resources.Env; } set { resources.Env = value; } }
+
+        public Cell()
+        {
+            organelles.Add(new Cytosol());
+            organelles.Add(new Mitochondrion());
+            organelles.Add(new Nucleus());
+            organelles.Add(new Membrane());
+            organelles.Add(new Lysosome());
+
+            resources = CellRessources.InitDefaults();
+            
+
+            // calcium baseline
+            caState.CytosolicCa = 0.0001; // 100 nM
+            caState.ER_Ca = 0.5;          // 0.5 mM
+        }
+
+        public void Step(double dt)
+        {
+            foreach (Organell organell in organelles)
+            {
+                organell.calculateRate(resources);
+            }
+
+            foreach (Organell organell in organelles)
+            {
+                organell.applyChanges(resources, dt);
+            }
+
+            CheckForDeath(dt);
+
+            time += dt;
+
+        }
+
+        private void CheckForDeath(double dt)
+        {
+            // Energie- und Calciumkritische Schwellen
+            const double ATP_MIN = 0.05;     // mM
+            const double CA_TOXIC = 0.002;   // 2 µM
+            const double WASTE_MAX = 5.0;    // mM
+
+            if (resources.Res.Energy.ATP < ATP_MIN || caState.CytosolicCa > CA_TOXIC || resources.Res.Protein.Waste > WASTE_MAX)
+            {
+                // langsamer Zelltod
+                if (rng.NextDouble() < 0.1 * dt)
+                    state = CellState.Apoptosis;
+            }
+
+            if (state == CellState.Apoptosis)
+            {
+                // Zelle verliert Ressourcen über Zeit
+                resources.Res.Energy.ATP *= (1.0 - 0.05 * dt);
+                resources.Res.Carbon.Glucose *= (1.0 - 0.03 * dt);
+                resources.Res.Protein.AminoAcids *= (1.0 - 0.02 * dt);
+            }
+        }
+
+        public cellInfo GetCellInfo()
+        {
+            return new cellInfo
+            {
+                time = this.time,
+                state = this.state,
+                resources = new Dictionary<string, double>
+                {
+                    { "Glucose", resources.Res.Carbon.Glucose },
+                    { "Oxygen", resources.Res.Oxygen },
+                    { "ATP", resources.Res.Energy.ATP },
+                    { "NAD", resources.Res.Energy.NAD },
+                    { "NADH", resources.Res.Energy.NADH },
+                    { "AminoAcids", resources.Res.Protein.AminoAcids }
+                },
+                caState = this.caState
+            };
+        }
+
+    }
+}

BaseCellSimulation/Cytosol.cs

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+using BaseCellSimulation.Enzyms;
+using BaseCellSimulation.Enzyms.Cytosol;
+using BaseCellSimulation.Enzyms.Cytosol.Ribosomen;
+
+
+namespace BaseCellSimulation
+{
+    /// <summary>
+    /// Cellliquid builds ATP and NADH out of Glucosis
+    /// </summary>
+    /// <param name="cellname"></param>
+    /// <param name="vmax"></param>
+    /// <param name="km"></param>
+    public class Cytosol : Organell
+    {
+        public readonly List<InternalEnzym> enzyms = new List<InternalEnzym>();
+
+        double ROS_base_rate = 1e-6;
+
+        private readonly string name;
+
+        private double rosProduction;
+
+        private double vOx;
+
+        public Cytosol() : this("Cytosol") { }
+
+        public Cytosol(string cellname)
+        {
+            name = cellname;
+
+            enzyms.Add(new Aldolase());
+            enzyms.Add(new AdenylateKinase());
+            enzyms.Add(new Enolase());
+            enzyms.Add(new GAPDH());
+            enzyms.Add(new Hexokinasis());
+            enzyms.Add(new Lactat_Dehydrogenase());
+            enzyms.Add(new PhosphoFructokinase());
+            enzyms.Add(new Phosphoglucose_Isomerase());
+            enzyms.Add(new Phosphoglycerat_Kinase());
+            enzyms.Add(new Phosphoglycerat_Mutase());
+            enzyms.Add(new Pyruvat_Kinase());
+            enzyms.Add(new Pyrophosphatase());
+            enzyms.Add(new Methionin_Adenosyltransferase());
+            enzyms.Add(new AHCY());
+            enzyms.Add(new Methioninsynthase());
+            enzyms.Add(new Ribosome());
+            enzyms.Add(new AminoacylTRNASynthetase());
+            enzyms.Add(new PeptidylTransferase());
+            enzyms.Add(new NucleosideDiphosphateKinase());
+        }
+
+        //Todo split in compute Rate and apply changes
+        // Stoichiometrie: 1 Glu -> 2 ATP + 2 NADH (simplyfied)
+        public void applyChanges(CellRessources Resources, double dt)
+        {
+            
+
+            foreach (InternalEnzym enzym in enzyms)
+            {
+                enzym.ApplyChanges(Resources, dt);
+            }
+
+            // Wenn O2 vorhanden: Pyruvat->CO2 + NADH via PDH/ TCA(vereinfacht)
+            // Simpler oxidativer Pfad (nur wenn genug O2) 
+            
+            double oxUsage = Math.Min(Resources.Res.Carbon.Pyruvate, vOx * dt); // skaliert mit O2
+            Resources.Res.Carbon.Pyruvate -= oxUsage;
+            Resources.Res.Carbon.CO2 += oxUsage;          // CO2 als Waste
+            Resources.Res.Oxygen -= 6.0 * oxUsage; // oxidativer Stoffwechsel erzeugt NADH (vereinfachung) und ATP (nicht durch Glykolyse)
+            Resources.TransferNADH(3.0 * oxUsage, false);   // Beispielzahl
+            Resources.RegenerateATP(12.0 * oxUsage);   // sehr grobe Näherung für oxidative Phosphorylierung
+
+            //ROS - Produktion: steigt mit hohem NADH/ NAD Verhältnis und mittlerem / hohem O2
+            Resources.Res.Ions.ROS += rosProduction * dt;
+
+            
+        }
+
+        public string getName()
+        {
+            return name;
+        }
+
+        public void calculateRate(CellRessources res)
+        {
+            foreach (InternalEnzym enzym in enzyms)
+            {
+                enzym.ComputeRate(res.Res);
+            }
+            double oxscaled = res.Res.Oxygen * 1000;
+            vOx = (oxscaled > 1e-3 && res.Res.Carbon.Pyruvate > 0) ? 0.5 * (oxscaled / (oxscaled + 5.0)) : 0.0;
+            if (oxscaled > 1e-3 && res.Res.Carbon.Pyruvate > 0)
+            {
+            }
+
+            double redoxRatio = (res.Res.Energy.NADH + 1e-12) / Math.Max(1e-12, res.Res.Energy.NAD);
+            rosProduction = ROS_base_rate * redoxRatio * (oxscaled / (oxscaled + 5.0));
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/AHCY.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class AHCY : InternalEnzym
+    {
+        public AHCY()
+        {
+            Km = 0.02;
+            Vmax = 0.3;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double dSAH = Math.Min(rate * dt, res.Res.Protein.SAH);
+            res.Res.Protein.SAH -= dSAH;
+            res.Res.Protein.Homocystein += dSAH;
+            res.Res.Protein.Adenosin += dSAH;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Protein.SAH);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/AdenylateKinase.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class AdenylateKinase : InternalEnzym
+    {
+        public AdenylateKinase() 
+        {
+            Km = 0.1;
+            Vmax = 5;
+            Keq = 1.1;
+
+            KmRange = new(0.01, 0.5);
+            VmaxRange = new(0.5, 15);
+            KeqRange = new(0.9, 1.2);
+        }
+
+        public double Keq { get; set; }
+
+        public ValueRange KeqRange;
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double d = rate * dt;
+
+            // Begrenzen, damit keine negativen Konzentrationen entstehen
+            if (d > 0.0)
+            {
+                // Vorwärtsrichtung: 2 ADP -> ATP + AMP
+                double limit = Math.Min(res.Res.Energy.ADP / 2.0, d);
+                res.Res.Energy.ADP -= 2.0 * limit;
+                res.Res.Energy.ATP += limit;
+                res.Res.Energy.AMP += limit;
+            }
+            else if (d < 0.0)
+            {
+                // Rückwärtsrichtung: ATP + AMP -> 2 ADP
+                double limit = Math.Min(Math.Min(res.Res.Energy.ATP, res.Res.Energy.AMP), -d);
+                res.Res.Energy.ADP += 2.0 * limit;
+                res.Res.Energy.ATP -= limit;
+                res.Res.Energy.AMP -= limit;
+            }
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            double numerator = res.Energy.ADP * res.Energy.ADP - res.Energy.ATP * res.Energy.AMP / Keq;
+            double denominator = Km * Km + res.Energy.ADP * res.Energy.ADP;
+
+            rate = Vmax * (numerator / denominator); // Nettoreaktionsrate in mM/s
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Aldolase.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class Aldolase : InternalEnzym
+    {
+        public Aldolase() 
+        {
+            Km = 0.1;
+            Vmax = 10;
+
+            KmRange = new(0.01, 0.3);
+            VmaxRange = new(2, 20);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double used = Math.Min(rate * dt, res.Res.Carbon.FBP);
+            res.Res.Carbon.FBP -= used;
+            res.Res.Carbon.GAP += 2 * used;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Carbon.FBP);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Enolase.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class Enolase : InternalEnzym
+    {
+        public Enolase() 
+        {
+            Km = 0.1;
+            Vmax = 10;
+
+            KmRange = new(0.01, 0.3);
+            VmaxRange = new(2, 25);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double used = Math.Min(rate * dt, res.Res.Carbon.PG2);
+
+            res.Res.Carbon.PG2 -= used;
+            res.Res.Carbon.PEP += used;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Carbon.PG2);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/GAPDH.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class GAPDH : InternalEnzym
+    {
+        public GAPDH()
+        {
+            Km = 0.1;
+            Km_NAD = 0.075;
+
+            Vmax = 10;
+
+            KmRange = new(0.01, 0.5);
+            VmaxRange = new(2, 25);
+            Km_NAD_Range = new(0.01, 0.2);
+        }
+        public double Km_NAD  { get; set; }
+
+        public ValueRange Km_NAD_Range { get; private set; }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double used = Math.Min(rate * dt, Math.Min(res.Res.Carbon.GAP, res.Res.Energy.NAD));
+            res.Res.Carbon.GAP     -= used;
+            res.Res.Carbon.PBG13   += used;
+            res.TransferNADH(used, false);
+            res.Res.Ions.Protons += 1.0 * used;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            rate = Vmax * (res.Carbon.GAP / (Km + res.Carbon.GAP)) * (res.Energy.NAD / (Km_NAD + res.Energy.NAD));
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Hexokinasis.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class Hexokinasis : InternalEnzym
+    {
+        public Hexokinasis() {
+            Km = 0.05;
+            Vmax = 5;
+
+            KmRange = new(0.01, 0.1);
+            VmaxRange = new(0.5, 20);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double used = Math.Min(rate * dt, Math.Min(res.Res.Carbon.Glucose, res.Res.Energy.ATP));
+            res.Res.Carbon.Glucose -= used;
+            res.Res.Carbon.G6P     += used;
+            res.ConsumeATP(used);
+            res.Res.Ions.Protons += used;
+        }
+
+        //todo noch machen dass atpberücksichtigt wird
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Carbon.Glucose);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Lactat_Dehydrogenase.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class Lactat_Dehydrogenase : InternalEnzym
+    {
+        public Lactat_Dehydrogenase()
+        {
+            Km = 0.5;
+            Vmax = 10;
+
+            KmRange = new(0.05,2);
+            VmaxRange = new(2, 25);
+
+            Km_NADH = 0.05;
+            Km_NADH_Range = new(0.005, 0.2);
+        }
+
+        public double Km_NADH { get; set; }
+
+        public ValueRange Km_NADH_Range { get; set; }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double used = Math.Min(rate * dt, Math.Min(res.Res.Carbon.Pyruvate, res.Res.Energy.NADH));
+
+            //LDH Lactat production and NAD+ regeneration
+            res.Res.Carbon.Pyruvate    -= used;
+            res.Res.Carbon.Lactate     += used;
+            res.TransferNADH(used,true);
+
+            //Consume Protons
+            res.Res.Ions.Protons -= 1.0 * used;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            double oxscaled = res.Oxygen * 1000;
+            double o2Factor = Math.Max(0.0, 1.0 - oxscaled / (oxscaled + 10.0));
+            rate = Vmax * o2Factor
+              * (res.Carbon.Pyruvate / (Km + res.Carbon.Pyruvate))
+              * (res.Energy.NADH / (Km_NADH + res.Energy.NADH));
+            
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Methionin_Adenosyltransferase.cs

@@ -0,0 +1,38 @@
+using BaseCellSimulation.Enzyms.Membrane;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using static System.Net.WebRequestMethods;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class Methionin_Adenosyltransferase : InternalEnzym
+    {
+        public double Km_ATP { get; set; }
+
+        public Methionin_Adenosyltransferase()
+        {
+            Km = 0.05;
+            Vmax = 0.5;
+            Km_ATP = 0.2;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double dSAM = Math.Min(rate * dt,res.Res.Energy.ATP);
+            res.Res.Protein.MET -= dSAM;
+            res.Res.Protein.SAM += dSAM;
+            res.Res.Energy.ATP -= dSAM;
+            res.Res.Phosphate.PPi += dSAM;
+            res.Res.Phosphate.Pi += dSAM;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            rate = Vmax * (res.Protein.MET / (Km + res.Protein.MET)) * (res.Energy.ATP / (Km_ATP + res.Energy.ATP));
+        }
+
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Methioninsynthase.cs

@@ -0,0 +1,50 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class Methioninsynthase : InternalEnzym
+    {
+        public Methioninsynthase()
+        {
+            Km = 0.015;
+            Vmax = 0.2;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            // Berechne tatsächlich mögliche Umwandlung
+            double dHcy = Math.Min(rate * dt, res.Res.Protein.Homocystein);
+            dHcy = Math.Min(dHcy, res.Res.Folate.MethylTHF);
+            dHcy = Math.Min(dHcy, res.Res.Cofactor.B12); // Co-Faktor limitierend
+
+            if (dHcy <= 0)
+                return;
+
+            // Verbrauch von Substraten
+            res.Res.Protein.Homocystein -= dHcy;
+            res.Res.Folate.MethylTHF -= dHcy;
+
+            // Cofaktor-B12 wird nicht dauerhaft verbraucht (Katalytisch)
+            // kann aber langsam inaktiviert werden, falls du das modellieren willst
+
+            // Bildung von Produkten
+            res.Res.Protein.MET += dHcy;
+            res.Res.Folate.THF += dHcy;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            // Aktivitätsfaktor abhängig vom verfügbaren B12
+            double cofactorEffect = Math.Clamp(res.Cofactor.B12 / 0.01, 0.0, 1.0);
+
+            // Michaelis-Menten über Homocystein
+            Michaelis_Menten(res.Protein.Homocystein);
+
+            rate *= cofactorEffect;
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/NucleosideDiphosphateKinase.cs

@@ -0,0 +1,50 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class NucleosideDiphosphateKinase : InternalEnzym
+    {
+        private const double k_eq = 0.25; // 0.25 / s → recht schnell, da NDK sehr aktiv ist
+
+        public NucleosideDiphosphateKinase()
+        {
+            Km = 0.05;    // unspezifisch, da das Enzym viele Nukleotide akzeptiert
+            Vmax = 1.0;   // fiktiver Maximalumsatz (mmol/L·s)
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            var energy = res.Res.Energy;
+
+            // --- Austausch zwischen ATP und GTP ---
+            double delta = (energy.ATP - energy.GTP) * k_eq * dt;
+
+            if (Math.Abs(delta) < 1e-9)
+                return;
+
+            // Begrenzung: kein negativer Pool
+            if (delta > 0)
+            {
+                delta = Math.Min(delta, energy.ATP);
+            }
+            else
+            {
+                delta = Math.Max(delta, -energy.GTP);
+            }
+
+            // Umsetzung: ATP -> GTP oder umgekehrt
+            energy.ATP -= delta;
+            energy.GTP += delta;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            double diff = Math.Abs(res.Energy.ATP - res.Energy.GTP);
+            Michaelis_Menten(diff);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/PhosphoFructokinase.cs

@@ -0,0 +1,42 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using static System.Net.WebRequestMethods;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class PhosphoFructokinase : InternalEnzym
+    {
+        public PhosphoFructokinase()
+        {
+            Km = 0.2;
+            Vmax = 7;
+
+            KmRange = new(0.05, 0.5);
+            VmaxRange = new(1, 25);
+        }
+
+        public double Ki_ATP_PFK    { get; set; }
+        public double Ka_AMP_PFK    { get; set; }
+        public double h_AMP         { get; set; }
+        public double h_ATP         { get; set; }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double used = Math.Min(rate * dt, Math.Min(res.Res.Energy.ATP, res.Res.Carbon.F6P));
+            res.Res.Carbon.F6P     -= used;
+            res.Res.Carbon.FBP     += used;
+            res.ConsumeATP(used);
+            res.Res.Ions.Protons += used;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            double inhibition = 1.0 / (1.0 + Math.Pow(res.Energy.ATP / Ki_ATP_PFK, h_ATP)); // Hemmung durch ATP
+            double activation = 1.0 + Math.Pow(res.Energy.AMP / Ka_AMP_PFK, h_AMP);         // Aktivierung durch AMP
+            rate = Michaelis_Menten(res.Carbon.F6P, Vmax * inhibition * activation, Km);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Phosphoglucose_Isomerase.cs

@@ -0,0 +1,32 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class Phosphoglucose_Isomerase : InternalEnzym
+    {
+        public Phosphoglucose_Isomerase()
+        {
+            Km = 0.1;
+            Vmax = 10;
+
+            KmRange = new(0.05, 0.2);
+            VmaxRange = new(0.5, 30);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double used = Math.Min(rate * dt, res.Res.Carbon.G6P);
+            res.Res.Carbon.G6P -= used;
+            res.Res.Carbon.F6P += used;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Carbon.G6P);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Phosphoglycerat_Kinase.cs

@@ -0,0 +1,33 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class Phosphoglycerat_Kinase : InternalEnzym
+    {
+        public Phosphoglycerat_Kinase()
+        {
+            Vmax = 10;
+            Km = 0.1;
+
+            KmRange = new(0.01, 0.3);
+            VmaxRange = new(2, 30);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double used = Math.Min(rate * dt, res.Res.Carbon.PBG13);
+            res.Res.Carbon.PBG13 -= used;
+            res.Res.Carbon.PG3 += used;
+            res.RegenerateATP(used);
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Carbon.PBG13);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Phosphoglycerat_Mutase.cs

@@ -0,0 +1,32 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class Phosphoglycerat_Mutase : InternalEnzym
+    {
+        public Phosphoglycerat_Mutase()
+        {
+            Km = 0.1;
+            Vmax = 10;
+
+            VmaxRange = new(2, 30);
+            KmRange = new(0.01, 0.3);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double used = Math.Min(rate * dt, res.Res.Carbon.PG3);
+            res.Res.Carbon.PG3 -= used;
+            res.Res.Carbon.PG2 += used;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Carbon.PG3);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Pyrophosphatase.cs

@@ -0,0 +1,32 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Security.Cryptography;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class Pyrophosphatase : InternalEnzym
+    {
+        public Pyrophosphatase()
+        {
+            Vmax = 2.0;
+            Km = 0.01;
+
+            VmaxRange = new(1, 10);
+            KmRange = new(0.001, 0.05);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double dPPi = Math.Max(rate, res.Res.Phosphate.PPi);
+            res.HydrolyzePPi(dPPi);
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Phosphate.PPi);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Pyruvat_Kinase.cs

@@ -0,0 +1,33 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol
+{
+    public class Pyruvat_Kinase : InternalEnzym
+    {
+        public Pyruvat_Kinase() 
+        {
+            Km = 0.1;
+            Vmax = 10;
+
+            KmRange = new(0.01, 0.3);
+            VmaxRange = new(2, 25);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double used = Math.Min(rate * dt, res.Res.Carbon.PEP);
+            res.Res.Carbon.PEP         -= used;
+            res.Res.Carbon.Pyruvate    += used;
+            res.RegenerateATP(used);
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Carbon.PEP);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Ribosomen/AminoacylTRNASynthetase.cs

@@ -0,0 +1,34 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol.Ribosomen
+{
+    public class AminoacylTRNASynthetase : InternalEnzym
+    {
+        public AminoacylTRNASynthetase()
+        {
+            Km = 0.1;
+            Vmax = 1.5;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double dAAtRNA = Math.Min(rate * dt, Math.Min(res.Res.Protein.AminoAcids, res.Res.Protein.tRNA));
+            dAAtRNA = Math.Min(dAAtRNA, res.Res.Energy.ATP);
+
+            res.Res.Protein.AminoAcids -= dAAtRNA;
+            res.Res.Protein.tRNA -= dAAtRNA;
+            res.Res.Protein.Aminoacyl_tRNA += dAAtRNA;
+            res.ConsumeATP(dAAtRNA);
+
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Protein.tRNA);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Ribosomen/PeptidylTransferase.cs

@@ -0,0 +1,32 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol.Ribosomen
+{
+    public class PeptidylTransferase : InternalEnzym
+    {
+        public PeptidylTransferase()
+        {
+            Km = 0.05;
+            Vmax = 5.0;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double dPeptide = Math.Min(rate * dt, Math.Min(res.Res.Protein.Aminoacyl_tRNA, res.Res.Energy.GTP));
+
+            res.Res.Protein.Aminoacyl_tRNA -= dPeptide;
+            res.Res.Protein.FunctionalProteins += dPeptide;
+            res.Res.Energy.GTP -= dPeptide;
+
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Protein.Aminoacyl_tRNA);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Ribosomen/Ribosome.cs

@@ -0,0 +1,103 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol.Ribosomen
+{
+    public class Ribosome : InternalEnzym
+    {
+        private TranslationFactor initiation;
+        private TranslationFactor elongation;
+        private TranslationFactor termination;
+
+        private const double ProteinPermRNA = 20.0;
+
+        int ribosomenState = 0;
+
+        public Ribosome()
+        {
+            Km = 0.5;    // fiktiv (abhängig von mRNA)
+            Vmax = 10.0; // z. B. 10 Aminosäuren pro Sekunde
+            initiation = new TranslationFactor(TranslationFactor.FactorType.Initiation);
+            elongation = new TranslationFactor(TranslationFactor.FactorType.Elongation);
+            termination = new TranslationFactor(TranslationFactor.FactorType.Termination);
+        }
+
+        private double availableAA = 0;
+        private double dProtein = 0;
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            int safety = 0;
+            while (safety++ < 10)
+            {
+                switch (ribosomenState)
+                {
+
+                    case 0:
+                        availableAA = res.Res.Protein.AminoAcids;
+                        dProtein = rate * dt;
+                        // Translation start -> Initiationsfaktoren verbrauchen GTP
+                        initiation.ApplyChanges(res, dt * 0.5);
+                        if (initiation.TranslationSpeed > 0)
+                        {
+                            dProtein = Math.Min(initiation.TranslationSpeed, dProtein);
+                            dProtein = Math.Min(dProtein, Math.Min(res.Res.Protein.mRNA, availableAA));
+                            res.Res.Protein.AminoAcids -= dProtein;
+                            res.Res.Protein.FunctionalProteins += dProtein;
+                            ribosomenState = 1;
+                        }
+                        else return;
+                        break;
+                    case 1:
+                        elongation.ApplyChanges(res, dt * dProtein * 0.1);
+                        if (elongation.TranslationSpeed > 0)
+                        {
+                            dProtein = Math.Min(elongation.TranslationSpeed, dProtein);
+                            // mRNA-Abnutzung: jede mRNA kann nur begrenzt oft benutzt werden
+                            double used_mRNA = dProtein / ProteinPermRNA;
+                            res.Res.Protein.mRNA -= used_mRNA;
+
+                            // Abbauprodukte: ein Teil recycelt, ein Teil wird zu Waste
+                            double degraded = used_mRNA * 0.8;
+                            double lost = used_mRNA * 0.2;
+                            res.Res.Protein.Nucleotides += degraded;  // Rückgewinn von Basen
+                            res.Res.Protein.Waste += lost;            // Restliche RNA-Fragmente als Zellabfall
+                            ribosomenState = 2;
+                        }
+
+                        else return;
+                        break;
+
+                    case 2:
+                        termination.ApplyChanges(res, dt * 0.01 * dProtein);
+                        if (termination.TranslationSpeed > 0)
+                        {
+                            res.ConsumeATP(dProtein * 4); // z. B. 4 ATP pro Peptidbindung  -> ADP 
+                            ribosomenState = 0;
+                        }
+                        else return; 
+
+                        break;
+                            
+                }
+            }
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            if (ribosomenState == 0) { 
+                if (res.Protein.AminoAcids <= 0.0 || res.Protein.mRNA <= 0.0)
+                    return;
+
+                double availablemRNA = res.Protein.mRNA;
+                Michaelis_Menten(availablemRNA);
+                initiation.ComputeRate(res);
+                elongation.ComputeRate(res);
+                termination.ComputeRate(res);
+            }
+        }
+    }
+}

BaseCellSimulation/Enzyms/Cytosol/Ribosomen/TranslationFactor.cs

@@ -0,0 +1,43 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Cytosol.Ribosomen
+{
+    /*
+     * Faktor Aufgabe Energieverbrauch
+     * IF (Initiation Factors)	Ribosom startet Translation	1 GTP
+     * EF-Tu, EF-G (Elongation)	tRNA Positionierung, Translokation	1–2 GTP pro Zyklus
+     * RF (Release Factors)	Beendet Translation an Stoppcodon	1 GTP
+    */
+    internal class TranslationFactor : InternalEnzym
+    {
+        public enum FactorType { Initiation, Elongation, Termination }
+        public FactorType Type { get; }
+
+        public double TranslationSpeed;
+
+        public TranslationFactor(FactorType type)
+        {
+            Type = type;
+            Km = 0.1;
+            Vmax = 2.0;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Energy.GTP);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double used = Math.Min(rate * dt, res.Res.Energy.GTP);
+
+            res.Res.Energy.GTP -= used;
+            res.Res.Energy.GDP += used;
+            TranslationSpeed = used;
+        }
+    }
+}

BaseCellSimulation/Enzyms/Enzym.cs

@@ -0,0 +1,50 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms
+{
+    public abstract class Enzym
+    {
+        /// <summary>
+        /// mM/S
+        /// </summary>
+        public double Vmax { get; set; }
+        /// <summary>
+        /// mM
+        /// </summary>
+        public double Km { get; set; }
+
+        public ValueRange VmaxRange { get; protected set; }
+
+        public ValueRange KmRange { get; protected set; }
+
+        protected double rate; 
+
+        protected void Michaelis_Menten(double ressource)
+        {
+            rate = Michaelis_Menten(ressource, Vmax, Km);
+        }
+
+        protected double Michaelis_Menten(double consumable,double vmax, double km)
+        {
+            return (vmax * consumable) / (km + consumable);
+        }
+
+        public abstract void ApplyChanges(CellRessources res, double dt);
+    }
+
+    public abstract class InternalEnzym : Enzym
+    {
+        public abstract void ComputeRate(Resources res);
+    }
+
+    public abstract class MembranEnzyme : Enzym
+    {
+        public abstract double CalculateGradient(CellRessources res);
+
+        public abstract void ComputeRate(double gradient, EnviromentState Env);
+    }
+}

BaseCellSimulation/Enzyms/Lysosome/Cathepsin.cs

@@ -0,0 +1,34 @@
+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

@@ -0,0 +1,88 @@
+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

@@ -0,0 +1,31 @@
+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

@@ -0,0 +1,32 @@
+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

@@ -0,0 +1,32 @@
+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
+        }
+    }
+}

BaseCellSimulation/Enzyms/Membrane/GLUT/GLUT1.cs

@@ -0,0 +1,42 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Membrane.GLUT
+{
+    public class GLUT1 : MembranEnzyme
+    {
+        public GLUT1()
+        {
+            Km = 1.5; // Example Km value in mM
+            Vmax = 0.5; 
+
+            KmRange = new(1.0, 3.0);
+            VmaxRange = new(0.1, 10.0);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double flux = Math.Min(res.Env.Glucose, rate * dt);
+            res.Env.Glucose -= flux;
+            res.Res.Carbon.Glucose += flux;
+        }
+
+        public override double CalculateGradient(CellRessources res)
+        {
+            return res.Env.Glucose - res.Res.Carbon.Glucose;
+        }
+
+        public override void ComputeRate(double gradient, EnviromentState Env)
+        {
+            if (gradient <= 0) 
+            {
+                rate = 0;
+                return;
+            }
+            Michaelis_Menten(gradient);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Membrane/GLUT/GLUT2.cs

@@ -0,0 +1,21 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Membrane.GLUT
+{
+    public class GLUT2 : GLUT1
+    {
+        public GLUT2()
+        {
+            Km = 17.0; // Example Km value in mM
+            Vmax = 1.2;
+
+            KmRange = new(15.0, 20.0);
+            VmaxRange = new(1.0, 50.0);
+        }
+
+    }
+}

BaseCellSimulation/Enzyms/Membrane/GLUT/GLUT3.cs

@@ -0,0 +1,20 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Membrane.GLUT
+{
+    public class GLUT3 : GLUT1
+    {
+        public GLUT3()
+        {
+            Km = 1.0; 
+            Vmax = 0.8; 
+
+            KmRange = new(0.3, 1.0);
+            VmaxRange = new(0.5, 20.0);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Membrane/GLUT/GLUT4.cs

@@ -0,0 +1,36 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Membrane.GLUT
+{
+    public class GLUT4 : GLUT1
+    {
+        public GLUT4()
+        {
+            Km = 5.0; // Example Km value in mM for GLUT4
+            Vmax = 0.6; // Higher Vmax for GLUT4
+            ActivationThreshold = 0.3; // Example threshold for insulin activation
+
+            KmRange = new(4.0, 6.0);
+            VmaxRange = new(0.2, 15.0);
+        }
+
+        public double ActivationThreshold { get; set; }
+
+        public override void ComputeRate(double gradient, EnviromentState Env)
+        {
+            if (gradient <= 0)
+            {
+                rate = 0;
+                return;
+            }
+            // GLUT4 is insulin-responsive, so we can add an insulin factor
+            double insulinFactor = 0.5 * (Math.Tanh((Env.Insulin - ActivationThreshold) / 0.1) + 1.0); // Example: insulin increases rate up to 3x
+            Michaelis_Menten(gradient);
+            rate *= insulinFactor;
+        }
+    }
+}

BaseCellSimulation/Enzyms/Membrane/KLeakChannel.cs

@@ -0,0 +1,30 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Membrane
+{
+    public class KLeakChannel : MembranEnzyme
+    {
+        public double Permeability = 0.01; // 1/s, diffusionsbasiert
+
+        public override void ComputeRate(double gradient, EnviromentState env)
+        {
+            rate = Permeability * gradient;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double flux = rate * dt;
+            res.Res.Ions.K -= flux; // aus der Zelle raus
+            res.Env.K += flux;
+        }
+
+        public override double CalculateGradient(CellRessources res)
+        {
+            return res.Res.Ions.K - res.Env.K;
+        }
+    }
+}

BaseCellSimulation/Enzyms/Membrane/MCT.cs

@@ -0,0 +1,39 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Membrane
+{
+    public class MCT : MembranEnzyme
+    {
+        
+        public override double CalculateGradient(CellRessources res)
+        {
+            double hGradient = Math.Pow(10, -res.pH_in) / Math.Pow(10, -res.pH_ext);
+            return res.Res.Carbon.Lactate - res.Env.Lactate * hGradient;   
+        }
+
+        public override void ComputeRate(double Gradient, EnviromentState env)
+        {
+            if (Gradient <= 0)
+            {
+                rate = 0;
+                return;
+            }
+
+            Michaelis_Menten(Gradient);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double flux = rate * dt;
+
+            res.Res.Carbon.Lactate -= flux; // Laktat raus
+            res.Env.Lactate        += flux;
+            res.Res.Ions.Protons   -= flux;             // Protonen raus (Symport)
+            res.Env.Protons        += flux;
+        }
+    }
+}

BaseCellSimulation/Enzyms/Membrane/NCX.cs

@@ -0,0 +1,55 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Membrane
+{
+    /// <summary>
+    /// Na+/Ca2+ Exchanger (3 Na⁺ in / 1 Ca²⁺ out)
+    /// Einfaches Michaelis-Menten-basiertes Modell mit Gradienten
+    /// </summary>
+    public class NCX : MembranEnzyme
+    {
+        public double NaStoich = 3.0; // Na⁺ pro Ca²⁺
+        public double CaStoich = 1.0;
+
+        /// <summary>
+        /// Berechnet die Transport-Rate abhängig von zellinternen und externen Ionenkonzentrationen
+        /// </summary>
+        public override void ComputeRate(double gradient, EnviromentState env)
+        {
+
+            // Michaelis-Menten-ähnliche Sättigung
+            rate = Vmax * gradient / (Km + Math.Abs(gradient));
+        }
+
+        /// <summary>
+        /// Wendet den Transport auf die Zellressourcen an
+        /// </summary>
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double flux = rate * dt;
+
+            // Na+ in die Zelle
+            res.Res.Ions.Na += NaStoich * flux;
+            res.Env.Na -= NaStoich * flux;
+
+            // Ca2+ aus der Zelle
+            res.Res.Ca.CytosolicCa -= CaStoich * flux;
+            res.Env.Ca += CaStoich * flux;
+
+        }
+
+        public override double CalculateGradient(CellRessources res)
+        {
+            // Gradienten: innen - außen
+            double naGradient = res.Res.Ions.Na - res.Env.Na;       // mM
+            double caGradient = res.Res.Ca.CytosolicCa - res.Env.Ca;       // mM
+
+            // Richtung: positiv = Ca raus / Na rein
+            return (naGradient / NaStoich) - (caGradient / CaStoich);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Membrane/NaK_ATPase.cs

@@ -0,0 +1,43 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Membrane
+{
+    public class NaK_ATPase : MembranEnzyme
+    {
+        public double ATPperCycle = 1.0;
+        public double NaOutStoich = 3.0;
+        public double KInStoich = 2.0;
+
+        public override void ComputeRate(double gradient, EnviromentState env)
+        {
+            
+            // niedriger Gradient → höhere Rate
+            double effective = 1.0 / (1.0 + gradient);
+            rate = Vmax * effective;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double flux = rate * dt;
+
+            // Verbrauch von ATP
+            double atpNeeded = flux * ATPperCycle;
+            if (res.Res.Energy.ATP < atpNeeded) flux *= res.Res.Energy.ATP / atpNeeded;
+
+            res.Res.Ions.Na -= NaOutStoich * flux;   // Na raus
+            res.Res.Ions.K += KInStoich * flux;      // K rein
+            res.Env.Na += NaOutStoich * flux;
+            res.Env.K -= KInStoich * flux;
+            res.ConsumeATP(atpNeeded);
+        }
+
+        public override double CalculateGradient(CellRessources res)
+        {
+            return (res.Res.Ions.Na / res.Env.Na) * (res.Env.K / res.Res.Ions.K);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Membrane/PMCA.cs

@@ -0,0 +1,39 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Membrane
+{
+    // ----------------------------------------------------------
+    // 3. PMCA – Ca²⁺-ATPase (Ca raus, ATP-abhängig)
+    // ----------------------------------------------------------
+    public class PMCA : MembranEnzyme
+    {
+        public double ATPperCycle = 1.0;
+
+        public override void ComputeRate(double caCyt, EnviromentState env)
+        {
+            // klassisch: Michaelis-Menten mit Ca²⁺-Abhängigkeit
+            rate = Michaelis_Menten(caCyt, Vmax, Km);
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double flux = rate * dt;
+            double atpNeeded = flux * ATPperCycle;
+
+            if (res.Res.Energy.ATP < atpNeeded) flux *= res.Res.Energy.ATP / atpNeeded;
+
+            res.Res.Ca.CytosolicCa -= flux;    // Ca raus
+            res.Env.Ca += flux;
+            res.ConsumeATP(atpNeeded);
+        }
+
+        public override double CalculateGradient(CellRessources res)
+        {
+            return res.Res.Ca.CytosolicCa; // PMCA is not driven by a concentration gradient
+        }
+    }
+}

BaseCellSimulation/Enzyms/Mytochondrion/ANTTransporter.cs

@@ -0,0 +1,35 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+// Noch gemacht werden
+namespace BaseCellSimulation.Enzyms.Mytochondrion
+{
+    public class ANTTransporter : InternalEnzym
+    {
+        public ANTTransporter()
+        {
+            Vmax = 0.3;
+            Km = 0.02; // mM ADP
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double adpAvailable = res.Res.Energy.ADP;
+            double atpAvailable = res.Res.Energy.ATP;
+            double transportable = Math.Min(adpAvailable, rate * dt);
+            transportable = Math.Min(transportable, atpAvailable); // Sicherstellen, dass genug ATP zum Tausch vorhanden ist
+            if (transportable <= 0) return;
+            res.Res.Energy.ADP -= transportable;
+            res.Res.Energy.ATP += transportable;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            double adp = res.Energy.ADP;
+            Michaelis_Menten(adp);
+        }
+    }
+}

BaseCellSimulation/Enzyms/Mytochondrion/ATPSynthase.cs

@@ -0,0 +1,31 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Mytochondrion
+{
+    public class ATPSynthase : InternalEnzym
+    {
+        public ATPSynthase()
+        {
+            Vmax = 0.4;
+            Km = 0.05; // ADP
+        }
+
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+
+            double used = Math.Min(res.Res.Energy.ADP, rate * dt);
+            res.RegenerateATP(used);
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            double gradient = Math.Clamp(res.Energy.NADH / (res.Energy.NAD + 1e-9), 0.0, 5.0);
+            rate = Vmax * (gradient / (Km + gradient));
+        }
+    }
+}

BaseCellSimulation/Enzyms/Mytochondrion/OxPhosEnzyme.cs

@@ -0,0 +1,54 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Mytochondrion
+{
+    public class OxPhosEnzyme : InternalEnzym
+    {
+        public double PO_Ratio { get; set; } = 2.5;
+
+        public OxPhosEnzyme()
+        {
+            Vmax = 0.8;
+            Km = 0.01;
+
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double usedNADH = Math.Min(rate * dt, res.Res.Energy.NADH);
+            if (usedNADH <= 0) return;
+
+            res.TransferNADH(usedNADH, true);
+
+            double o2Consumed = 0.5 * usedNADH;
+            res.Res.Oxygen = Math.Max(0.0, res.Res.Oxygen - o2Consumed);
+
+            double atpMade = PO_Ratio * usedNADH;
+            res.RegenerateATP(atpMade);
+
+            // ROS-Produktion
+            double rosFactor = Math.Min(1.0, res.Res.Oxygen / 2.0);
+            res.Res.Ions.H2O2 += usedNADH * 0.001 * rosFactor;
+            res.Res.Protein.Waste += usedNADH * 0.001 * rosFactor;
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            double nadh = res.Energy.NADH;
+            Michaelis_Menten(nadh);
+
+            // Begrenzung durch O2
+            double o2Limit = Math.Min(1.0, res.Oxygen / 0.05);
+            rate *= o2Limit;
+
+            // ATP/ROS Feedback
+            double atpFactor = Math.Clamp(res.Energy.ATP / 0.5, 0.0, 1.0);
+            double wasteFactor = 1.0 / (1.0 + res.Protein.Waste / 10.0);
+            rate *= atpFactor * wasteFactor;
+        }
+    }
+}

BaseCellSimulation/Enzyms/Mytochondrion/PyruvateDehydrogenase.cs

@@ -0,0 +1,42 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Mytochondrion
+{
+    public class PyruvateDehydrogenase : InternalEnzym
+    {
+        public PyruvateDehydrogenase()
+        {
+            Vmax = 1.0; // mM/s
+            Km = 0.05;   // mM Pyruvat
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Carbon.Pyruvate);
+
+            // Aktivierung durch Ca²⁺
+            double ca = res.Ca.CytosolicCa;
+            double caBoost = 1.0 + 0.8 * (ca / (0.0005 + ca)); // bis ~1.8x Boost
+            rate *= caBoost;
+
+            // Hemmung durch hohes NADH/NAD+ Verhältnis oder ATP
+            double redox = res.Energy.NAD / (res.Energy.NAD + res.Energy.NADH + 1e-9);
+            double energy = res.Energy.ATP / (res.Energy.ATP + res.Energy.ADP + 1e-9);
+            rate *= redox * (1.0 - 0.5 * energy); // Hohe Energie hemmt
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double used = Math.Min(res.Res.Carbon.Pyruvate, rate * dt);
+
+            res.Res.Carbon.Pyruvate -= used;
+            res.Res.Carbon.AcetylCoA += used;
+            res.TransferNADH(used, false);
+            res.Res.Carbon.CO2 += used;
+        }
+    }
+}

BaseCellSimulation/Enzyms/Mytochondrion/TCA.cs

@@ -0,0 +1,35 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms.Mytochondrion
+{
+    public class TCAEnzyme : InternalEnzym
+    {
+        public TCAEnzyme()
+        {
+            Vmax = 0.1; // mM/s
+            Km = 0.02;  // mM Acetyl-CoA
+        }
+
+        public override void ComputeRate(Resources res)
+        {
+            Michaelis_Menten(res.Carbon.AcetylCoA);
+            // Abhängig vom Redoxstatus
+            double redox = res.Energy.NAD / (res.Energy.NAD + res.Energy.NADH + 1e-9);
+            rate *= redox;
+        }
+
+        public override void ApplyChanges(CellRessources res, double dt)
+        {
+            double used = Math.Min(res.Res.Carbon.AcetylCoA, rate * dt);
+            res.Res.Carbon.AcetylCoA -= used;
+            res.TransferNADH(2 * used, false);
+            //res.FADH2 += used;
+            res.Res.Energy.GTP += used; // optional
+            res.Res.Carbon.CO2 += 2 * used;
+        }
+    }
+}

BaseCellSimulation/Enzyms/Nucleus/DNA_Polymerase_Delta.cs

@@ -0,0 +1,33 @@
+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

@@ -0,0 +1,43 @@
+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

@@ -0,0 +1,29 @@
+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

@@ -0,0 +1,30 @@
+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

@@ -0,0 +1,33 @@
+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

@@ -0,0 +1,34 @@
+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

@@ -0,0 +1,32 @@
+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);
+        }
+    }
+}

BaseCellSimulation/Enzyms/VmaxCalculator.cs

@@ -0,0 +1,51 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation.Enzyms
+{
+    public static class VmaxCalculator
+    {
+        private const double Avogadro = 6.02214076e23; // mol⁻¹
+
+        /// <summary>
+        /// Berechnet Vmax (in mM/s) aus Enzymkinetik-Parametern.
+        /// </summary>
+        /// <param name="kcat">Turnover-Zahl des Enzyms (s⁻¹ pro Molekül)</param>
+        /// <param name="enzymeCount">Anzahl der Enzymmoleküle in der Zelle</param>
+        /// <param name="cellVolume_L">Zellvolumen in Litern (z. B. 1e-12 für typische Eukaryoten)</param>
+        /// <returns>Vmax in mM/s</returns>
+        public static double ComputeVmax(double kcat, double enzymeCount, double cellVolume_L)
+        {
+            // [E_total] = (enzymeCount / Avogadro) / cellVolume
+            double enzymeConcentration_M = (enzymeCount / Avogadro) / cellVolume_L; // mol/L
+            double vmax_M_per_s = kcat * enzymeConcentration_M;                    // mol/L/s
+
+            // Umrechnung auf mM/s
+            return vmax_M_per_s * 1000.0;
+        }
+
+        /// <summary>
+        /// Beispielausgabe für häufige Zellgrößen / Transporter.
+        /// </summary>
+        public static void Example()
+        {
+            // Beispielwerte: GLUT1, GLUT2, GLUT3, GLUT4
+            double cellVolume = 1e-12; // Liter (≈ typische Säugetierzelle)
+            double[] enzymeCounts = { 1e5, 1e6, 1e7 }; // niedrige, mittlere, hohe Expression
+            double[] kcats = { 100, 500, 1000 }; // plausible Turnover-Werte
+
+            foreach (var kcat in kcats)
+            {
+                foreach (var enz in enzymeCounts)
+                {
+                    double vmax = ComputeVmax(kcat, enz, cellVolume);
+                    Console.WriteLine($"kcat={kcat,5:F0}  Enzyme={enz:E0}  →  Vmax={vmax:F2} mM/s");
+                }
+            }
+        }
+    }
+
+}

BaseCellSimulation/Lysosome.cs

@@ -0,0 +1,61 @@
+using BaseCellSimulation.Enzyms;
+using BaseCellSimulation.Enzyms.Lysosome;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Resources;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation
+{
+    /// <summary>
+    /// Recicling center of the cell takes up waste and generates Amino acides and small amout of ATP
+    /// </summary>
+    /// <param name="cellname"></param>
+    /// <param name="decayRate"></param>
+    public class Lysosome : Organell
+    {
+        public readonly List<InternalEnzym> enzyms = new List<InternalEnzym>();
+
+        private readonly string name;
+
+        public Lysosome() : this("Lysosome") { }
+
+        public Lysosome(string cellname)
+        {
+            name = cellname;
+            enzyms.Add(new Cathepsin());
+            enzyms.Add(new GenericLysosomalEnzyme());
+            enzyms.Add(new LysosomalLipase());
+            enzyms.Add(new LysosomalNuclease());
+            enzyms.Add(new LysosomalPhosphatase());
+
+        }
+
+
+        public string getName()
+        {
+            return name;
+        }
+
+        public void applyChanges(CellRessources Resources, double dt)
+        {
+            
+
+            foreach (InternalEnzym enzym in enzyms)
+            {
+                enzym.ApplyChanges(Resources, dt);
+            }
+
+        }
+
+        public void calculateRate(CellRessources res)
+        {
+            foreach (InternalEnzym enzym in enzyms)
+            {
+                enzym.ComputeRate(res.Res);
+            }
+        }
+    }
+}

BaseCellSimulation/Membrane.cs

@@ -0,0 +1,70 @@
+using BaseCellSimulation.Enzyms;
+using BaseCellSimulation.Enzyms.Membrane;
+using BaseCellSimulation.Enzyms.Membrane.GLUT;
+
+namespace BaseCellSimulation
+{
+    /// <summary>
+    /// Cell membrane small leakage and passive disposal of waste
+    /// </summary>
+    /// <param name="cellname"></param>
+    /// <param name="glucoseImportRate"></param>
+    /// <param name="oxygenImportRate"></param>
+    /// <param name="wasteOuttakeRate"></param>
+    public class Membrane : Organell
+    {
+        public readonly List<MembranEnzyme> enzyms = new List<MembranEnzyme>();
+        public readonly List<GLUT1> glutTransporters = new List<GLUT1>();
+        private readonly string name;
+
+        public Membrane() : this("Membrane") { }
+
+        public Membrane(string cellname)
+        {
+            this.name = cellname;
+            enzyms.Add(new KLeakChannel());
+            enzyms.Add(new MCT());
+            enzyms.Add(new NaK_ATPase());
+            enzyms.Add(new NCX());
+            enzyms.Add(new PMCA());
+            // Add GLUT transporters
+            glutTransporters.Add(new GLUT1());
+        }
+
+        public string getName()
+        {
+            return name;
+        }
+
+        public void applyChanges(CellRessources res, double dt)
+        {
+
+            foreach (MembranEnzyme enzyme in enzyms)
+            {
+                enzyme.ApplyChanges(res, dt);
+            }
+            foreach (GLUT1 glut in glutTransporters)
+            {
+                glut.ApplyChanges(res, dt);
+            }
+            // --- 5. Kleine Verluste anderer Stoffe (Diffusionslecks) ---
+            res.Res.Carbon.Glucose = Math.Max(0, res.Res.Carbon.Glucose - 0.001 * dt);
+            res.Res.Oxygen = Math.Max(0, res.Res.Oxygen - 0.001 * dt);
+        }
+
+        public void calculateRate(CellRessources res)
+        {
+            foreach (MembranEnzyme enzyme in enzyms)
+            {
+                double gradient = enzyme.CalculateGradient(res);
+                enzyme.ComputeRate(gradient, res.Env);
+            }
+            double glutGradient = glutTransporters[0].CalculateGradient(res);
+
+            foreach (GLUT1 glut in glutTransporters)
+            {
+                glut.ComputeRate(glutGradient, res.Env);
+            }
+        }
+    }
+}

BaseCellSimulation/Mitochondrion.cs

@@ -0,0 +1,67 @@
+using BaseCellSimulation.Enzyms;
+using BaseCellSimulation.Enzyms.Mytochondrion;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using static System.Runtime.InteropServices.JavaScript.JSType;
+
+namespace BaseCellSimulation
+{
+    /// <summary>
+    /// Powerplant of the cell generates ATP out od NADH and Oxygen
+    /// </summary>
+    /// <param name="cellName"></param>
+    /// <param name="oxPhosVmax"></param>
+    /// <param name="oxPhosKm"></param>
+    /// <param name="pO_Ratio"></param>
+    public class Mitochondrion : Organell
+    {
+        public List<Enzym> Enzyms { get; private set; } = new List<Enzym>();
+
+
+
+        private readonly string name;
+
+        public Mitochondrion() : this("Mitochondrion") {}
+
+        public Mitochondrion(string cellName)
+        {
+            name = cellName;
+            Enzyms.Add(new PyruvateDehydrogenase());
+            //Enzyms.Add(new Enzyms.Mytochondrion.ANTTransporter());
+            Enzyms.Add(new OxPhosEnzyme());
+            Enzyms.Add(new ATPSynthase());
+            Enzyms.Add(new TCAEnzyme());
+        }
+
+
+        public string getName()
+        {
+            return name;
+        }
+
+        public void applyChanges(CellRessources Resources, double dt)
+        {
+            
+
+            foreach (Enzym enzym in Enzyms)
+            {
+                enzym.ApplyChanges(Resources, dt);
+            }
+            
+        }
+
+        public void calculateRate(CellRessources res)
+        {
+            foreach (Enzym enzym in Enzyms)
+            {
+                if (enzym is InternalEnzym internalEnzym)
+                {
+                    internalEnzym.ComputeRate(res.Res);
+                }
+            }
+        }
+    }
+}

BaseCellSimulation/Nucleus.cs

@@ -0,0 +1,61 @@
+using BaseCellSimulation.Enzyms;
+using BaseCellSimulation.Enzyms.Nucleus;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation
+{
+    /// <summary>
+    /// Cell Core produces RNA uses ATP generates small amount of waste
+    /// </summary>
+    /// <param name="cellname"></param>
+    /// <param name="transcriptionRate"></param>
+    /// <param name="atpPerNucloide"></param>
+    public class Nucleus : Organell
+    {
+        public List<InternalEnzym> enzyms = new List<InternalEnzym>();
+
+        private readonly string name;
+
+        public Nucleus() : this("Nucleus") { }
+
+        public Nucleus(string cellname)
+        {
+            name = cellname;
+            enzyms.Add(new DNA_Polymerase_Delta());
+            enzyms.Add(new DNMT1());
+            enzyms.Add(new HistoneAcetyltransferase());
+            enzyms.Add(new HistoneDeacetylase());
+            enzyms.Add(new PARP1());
+            enzyms.Add(new Topoisomerase_II());
+            enzyms.Add(new RNA_Polymerase_II());
+
+        }
+
+
+        public string getName()
+        {
+            return name;
+        }
+
+        public void applyChanges(CellRessources Resources, double dt)
+        {
+            
+            foreach (InternalEnzym enzym in enzyms)
+            {
+                enzym.ApplyChanges(Resources, dt);
+            }
+        }
+
+        public void calculateRate(CellRessources res)
+        {
+            foreach (InternalEnzym enzym in enzyms)
+            {
+                enzym.ComputeRate(res.Res);
+            }
+        }
+    }
+}

BaseCellSimulation/Organell.cs

@@ -0,0 +1,397 @@
+using System;
+
+namespace BaseCellSimulation
+{
+    /// <summary>
+    /// Container, der die aktuellen Ressourcen einer Zelle hält und Hilfsfunktionen bietet.
+    /// </summary>
+    public class CellRessources
+    {
+        public Resources Res;
+        public EnviromentState Env = new();
+
+        // pH in mM-basiertem Hilfsformat (vereinfachte Umrechnung):
+        public double pH_in => 3.0 - Math.Log10(Res.Ions.Protons + 1e-12);
+        public double pH_ext => 3.0 - Math.Log10(Env.Protons + 1e-12);
+
+        // --- Hilfsfunktionen (unverändert / kommentiert) ---
+
+        public double GetEnergyLevel()
+        {
+            double totalATP = Res.Energy.ATP + 0.5 * Res.Energy.ADP + 0.1 * Res.Energy.AMP;
+            double redoxEnergy = 0.3 * Res.Energy.NADH;
+            double energy = totalATP + redoxEnergy;
+            return Math.Clamp(energy / 5.0, 0.0, 1.0);
+        }
+
+        public double EnergyCharge
+        {
+            get
+            {
+                double atp = Res.Energy.ATP;
+                double adp = Res.Energy.ADP;
+                double amp = Res.Energy.AMP;
+                double total = atp + adp + amp;
+                if (total < 1e-12) return 0.0;
+                return (atp + 0.5 * adp) / total;
+            }
+        }
+
+        public bool IsEnergyDeficient(double threshold = 0.3)
+        {
+            return Res.Energy.ATP < threshold;
+        }
+
+        public double GetRedoxRatio()
+        {
+            double denominator = Math.Max(Res.Energy.NADH, 1e-9);
+            return Res.Energy.NAD / denominator;
+        }
+
+        public double GetStressLevel()
+        {
+            double stress = Res.Protein.Waste * 0.1 + Res.Ions.ROS * 0.5 + Res.Ions.Protons * 0.05;
+            return Math.Clamp(stress, 0.0, 1.0);
+        }
+
+        public bool IsUnderStress(double threshold = 0.5)
+        {
+            return GetStressLevel() > threshold;
+        }
+
+        public void ConsumeATP(double amount, bool toAMP = false)
+        {
+            if (Res.Energy.ATP < amount) amount = Res.Energy.ATP;
+            Res.Energy.ATP -= amount;
+            if (toAMP)
+            {
+                Res.Energy.AMP += amount;
+                Res.Phosphate.PPi += amount;
+            }
+            else
+            {
+                Res.Energy.ADP += amount;
+                Res.Phosphate.Pi += amount;
+            }
+        }
+
+        public void RegenerateATP(double amount, bool fromAMP = false)
+        {
+            if (fromAMP)
+            {
+                if (Res.Energy.AMP < amount) amount = Res.Energy.AMP;
+                if (Res.Phosphate.Pi < 2 * amount) amount = Res.Phosphate.Pi / 2;
+                Res.Energy.AMP -= amount;
+                Res.Phosphate.Pi -= 2 * amount;
+            }
+            else
+            {
+                if (Res.Energy.ADP < amount) amount = Res.Energy.ADP;
+                if (Res.Phosphate.Pi < amount) amount = Res.Phosphate.Pi;
+                Res.Energy.ADP -= amount;
+                Res.Phosphate.Pi -= amount;
+            }
+            Res.Energy.ATP += amount;
+        }
+
+        public void HydrolyzePPi(double amount)
+        {
+            if (Res.Phosphate.PPi < amount) amount = Res.Phosphate.PPi;
+            Res.Phosphate.PPi -= amount;
+            Res.Phosphate.Pi += 2 * amount;
+        }
+
+        public void TransferNADH(double amount, bool oxidize)
+        {
+            if (oxidize)
+            {
+                if (Res.Energy.NADH < amount) amount = Res.Energy.NADH;
+                Res.Energy.NADH -= amount;
+                Res.Energy.NAD += amount;
+            }
+            else
+            {
+                if (Res.Energy.NAD < amount) amount = Res.Energy.NAD;
+                Res.Energy.NAD -= amount;
+                Res.Energy.NADH += amount;
+            }
+        }
+
+        // --- Initialisierung mit plausiblen Startwerten ---
+        /// <summary>
+        /// Erzeugt eine CellRessources-Instanz mit vernünftigen Startwerten (grobe physiologische Annahmen).
+        /// Alle Werte in mM, falls nicht anders kommentiert.
+        /// </summary>
+        public static CellRessources InitDefaults()
+        {
+            var cr = new CellRessources();
+
+            // Energie-Pool (ATP/ADP/AMP etc.) — typisch: ATP im mm-Bereich
+            cr.Res.Energy.ATP = 2.5;    // mM, Gesamt-ATP (typischer Ruhewert 1-5 mM)
+            cr.Res.Energy.ADP = 0.5;    // mM
+            cr.Res.Energy.AMP = 0.05;   // mM
+            cr.Res.Energy.NAD = 1.0;    // mM (oxidierte Form)
+            cr.Res.Energy.NADH = 0.1;   // mM (reduzierte Form)
+            cr.Res.Energy.GTP = 0.5;    // mM
+            cr.Res.Energy.GDP = 0.05;   // mM
+
+            // Phosphate
+            cr.Res.Phosphate.Pi = 10.0;  // mM (anorganisches Phosphat)
+            cr.Res.Phosphate.PPi = 0.01; // mM (Pyrophosphat, klein)
+
+            // Carbon- / Glykolyse-Pool (vereinfachte Startwerte)
+            cr.Res.Carbon.Glucose = 1.0;   // mM intrazellulär (abhängig von Aufnahme)
+            cr.Res.Carbon.G6P = 0.05;
+            cr.Res.Carbon.F6P = 0.02;
+            cr.Res.Carbon.FBP = 0.005;
+            cr.Res.Carbon.GAP = 0.01;
+            cr.Res.Carbon.PBG13 = 0.005;
+            cr.Res.Carbon.PG3 = 0.02;
+            cr.Res.Carbon.PG2 = 0.01;
+            cr.Res.Carbon.PEP = 0.01;
+            cr.Res.Carbon.Pyruvate = 0.1;
+            cr.Res.Carbon.Lactate = 1.0;
+            cr.Res.Carbon.CO2 = 0.1;
+            cr.Res.Carbon.AcetylCoA = 0.02;
+
+            // Proteine & Nukleotid-Pool
+            cr.Res.Protein.AminoAcids = 5.0;         // mM frei verfügbare Aminosäuren
+            cr.Res.Protein.FunctionalProteins = 100; // arbitrary, relative Konzentration (nicht streng mM)
+            cr.Res.Protein.Waste = 0.1;              // kleiner Startwert
+            cr.Res.Protein.NucleicAcids = 10.0;
+            cr.Res.Protein.Nucleotides = 5.0;
+            cr.Res.Protein.NTP = 2.0;
+            cr.Res.Protein.dNTP = 0.05;
+            cr.Res.Protein.mRNA = 0.01;
+            cr.Res.Protein.DNA_damage = 0.0;
+            cr.Res.Protein.AcetylCoA = 0.02;
+            cr.Res.Protein.SAM = 0.1;
+            cr.Res.Protein.MET = 0.1;
+            cr.Res.Protein.SAH = 0.01;
+            cr.Res.Protein.Homocystein = 0.01;
+            cr.Res.Protein.Adenosin = 0.1;
+            cr.Res.Protein.tRNA = 0.05;
+            cr.Res.Protein.Aminoacyl_tRNA = 0.02;
+
+            // Ionen
+            cr.Res.Ions.Protons = 0.0001; // mM -> entspricht ~pH7 (vereinfachte Umrechnung)
+            cr.Res.Ions.ROS = 0.001;      // kleine ROS-Basislast
+            cr.Res.Ions.Na = 10.0;        // Intrazelluläres Na+ ~ 5-15 mM (Zelltypabhängig)
+            cr.Res.Ions.K = 140.0;        // Intrazelluläres K+ ~ 140 mM
+            cr.Res.Ions.H2O2 = 0.0001;
+
+            // Cofaktoren / Folate
+            cr.Res.Cofactor.B12 = 1e-6;
+            cr.Res.Folate.THF = 0.01;
+            cr.Res.Folate.MethylTHF = 0.005;
+
+            // Zellkern-Ressourcen (vereinfachte Defaults)
+            cr.Res.Nucleus.ChromatinAccessibility = 0.5;
+            cr.Res.Nucleus.ReplicationProgress = 0.0;
+
+            // Calcium-Zustand (CellCaState hat sinnvolle Defaultwerte)
+            cr.Res.Ca = new CellCaState()
+            {
+                CytosolicCa = 0.0001, // 100 nM -> 0.0001 mM
+                ER_Ca = 0.5,
+                LeakK = 0.001,
+                SERCA_Vmax = 0.01,
+                SERCA_Km = 0.0002,
+                SERCA_ATP_per_twoCa = 1.0,
+                LysosomeActivity = 0.1
+            };
+
+            // Sonstige Ressourcen
+            cr.Res.Oxygen = 0.2; // mM Lösungssauerstoff (abhängig von Umgebung)
+            cr.Res.Heat = 0.0;
+            cr.Res.Lipids = 10.0;
+            cr.Res.PhosphorylatedSubstrates = 1.0;
+
+            // Umgebung / Extrazellulärwerte
+            cr.Env.Glucose = 5.0;   // Blutglukose ~5 mM
+            cr.Env.Oxygen = 0.2;    // mM
+            cr.Env.Waste = 0.0;
+            cr.Env.Lactate = 1.0;
+            cr.Env.Insulin = 0.0;
+            cr.Env.Protons = 0.0001; // ähnlich pH 7
+            cr.Env.Na = 140.0;       // extrazelluläres Na+ ~ 140 mM
+            cr.Env.K = 4.0;          // extrazelluläres K+ ~ 4-5 mM
+            cr.Env.Ca = 1.2;         // extrazelluläres Ca2+ ~1.1-1.3 mM
+
+            return cr;
+        }
+    }
+
+    // ------------------------------------------------------------
+    // Datendefinitionen (geordnet und kommentiert)
+    // ------------------------------------------------------------
+
+    /// <summary>Energiemengen: ATP/ADP/AMP + NAD/NADH + GTP/GDP</summary>
+    public struct EnergyPool
+    {
+        public double ATP;
+        public double ADP;
+        public double AMP;
+        public double NAD;
+        public double NADH;
+        public double GTP;
+        public double GDP { get; internal set; }
+    }
+
+    /// <summary>Inorganische Phosphate</summary>
+    public struct Phosphate
+    {
+        public double Pi;  // anorganisches Phosphat
+        public double PPi; // Pyrophosphat
+    }
+
+    /// <summary>Kohlenstoff- / Glykolyse-Intermediaten</summary>
+    public struct CarbonPool
+    {
+        public double Glucose;
+        public double G6P;
+        public double F6P;
+        public double FBP;
+        public double GAP;
+        public double PBG13;
+        public double PG3;
+        public double PG2;
+        public double PEP;
+        public double Pyruvate;
+        public double Lactate;
+        public double CO2;
+        public double AcetylCoA;
+    }
+
+    /// <summary>Proteine, Nukleotide, mRNA, etc.</summary>
+    public struct ProteinPool
+    {
+        public double AminoAcids;
+        public double FunctionalProteins;
+        public double Waste;
+        public double NucleicAcids;
+        public double Nucleotides;
+        public double NTP;
+        public double dNTP;
+        public double mRNA;
+        public double DNA_damage;
+        public double AcetylCoA;
+        public double SAM;
+        public double MET;
+        public double SAH;
+        public double Homocystein;
+        public double Adenosin;
+        internal double tRNA;
+        internal double Aminoacyl_tRNA;
+    }
+
+    /// <summary>Ionen und kleine Signalmoleküle</summary>
+    public struct IonPool
+    {
+        public double Protons; // H+ (vereinfachte Einheit mM)
+        public double ROS;     // reactive oxygen species
+        public double Na;
+        public double K;
+        public double H2O2;
+    }
+
+    public struct Cofactor
+    {
+        public double B12;
+    }
+
+    public struct Folates
+    {
+        public double THF { get; internal set; }
+        public double MethylTHF { get; internal set; }
+    }
+
+    public struct NucleusRessources
+    {
+        public double ChromatinAccessibility;
+        public double ReplicationProgress;
+    }
+
+    /// <summary>Gesammelte Ressourcen einer Zelle</summary>
+    public struct Resources
+    {
+        public EnergyPool Energy;
+        public Phosphate Phosphate;
+        public CarbonPool Carbon;
+        public ProteinPool Protein;
+        public IonPool Ions;
+        public CellCaState Ca;
+        public NucleusRessources Nucleus;
+        public Cofactor Cofactor;
+        public Folates Folate;
+
+        public double Oxygen;
+        public double Heat;
+        public double Lipids;
+        public double PhosphorylatedSubstrates;
+    }
+
+    public enum CellState { Resting, Dividing, Apoptosis }
+
+    public enum CAToxicity { None, Mild, Severe, Lethal }
+
+    public class EnviromentState
+    {
+        public double Glucose;
+        public double Oxygen;
+        public double Waste;
+        public double Lactate;
+        public double Insulin;
+        public double Protons;
+        public double Na;
+        public double K;
+        public double Ca;
+    }
+
+    /// <summary>
+    /// Ein einfaches Modell des zellulären Calcium-Haushalts.
+    /// Werte in mM; Defaultwerte sind phänotypisch realistisch gewählt.
+    /// </summary>
+    public struct CellCaState
+    {
+        public double CytosolicCa { get; set; } // zytosolisches Ca (mM), üblich ~100 nM = 0.0001 mM
+        public double ER_Ca { get; set; }       // ER Calcium (mM)
+        public double LeakK { get; set; }       // Leck-Koeffizient
+        public double SERCA_Vmax { get; set; }
+        public double SERCA_Km { get; set; }    // Km in mM
+        public double SERCA_ATP_per_twoCa { get; set; }
+        public double LysosomeActivity { get; internal set; }
+
+        public const double ToxicityThresholdMild = 0.001;   // 1 µM
+        public const double ToxicityThresholdSevere = 0.01;  // 10 µM
+        public const double ToxicityThresholdLethal = 0.1;   // 100 µM
+
+        public CellCaState()
+        {
+            CytosolicCa = 0.0001;
+            ER_Ca = 0.5;
+            LeakK = 0.001;
+            SERCA_Vmax = 0.01;
+            SERCA_Km = 0.0002;
+            SERCA_ATP_per_twoCa = 1.0;
+            LysosomeActivity = 0.1;
+        }
+
+        public CAToxicity getCaToxicityLevel()
+        {
+            if (CytosolicCa >= ToxicityThresholdLethal) return CAToxicity.Lethal;
+            else if (CytosolicCa >= ToxicityThresholdSevere) return CAToxicity.Severe;
+            else if (CytosolicCa >= ToxicityThresholdMild) return CAToxicity.Mild;
+            else return CAToxicity.None;
+        }
+    }
+
+    public interface Organell
+    {
+        void applyChanges(CellRessources Resources, double dt);
+
+        void calculateRate(CellRessources res);
+
+        string getName();
+    }
+}

BaseCellSimulation/ValueRange.cs

@@ -0,0 +1,20 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace BaseCellSimulation
+{
+    public struct ValueRange
+    {
+        public double Start;
+        public double End;
+
+        public ValueRange(double start, double end)
+        {
+            Start = start;
+            End = end;
+        }
+    }
+}

CellSimulation.Desktop/CellSimulation.Desktop.csproj

@@ -0,0 +1,27 @@
+<Project Sdk="Microsoft.NET.Sdk">
+  <PropertyGroup>
+    <OutputType>WinExe</OutputType>
+    <!--If you are willing to use Windows/MacOS native APIs you will need to create 3 projects.
+    One for Windows with net9.0-windows TFM, one for MacOS with net9.0-macos and one with net9.0 TFM for Linux.-->
+    <TargetFramework>net9.0</TargetFramework>
+    <Nullable>enable</Nullable>
+    <BuiltInComInteropSupport>true</BuiltInComInteropSupport>
+  </PropertyGroup>
+
+  <PropertyGroup>
+    <ApplicationManifest>app.manifest</ApplicationManifest>
+  </PropertyGroup>
+
+  <ItemGroup>
+    <PackageReference Include="Avalonia.Desktop" />
+    <!--Condition below is needed to remove Avalonia.Diagnostics package from build output in Release configuration.-->
+    <PackageReference Include="Avalonia.Diagnostics" >
+      <IncludeAssets Condition="'$(Configuration)' != 'Debug'">None</IncludeAssets>
+      <PrivateAssets Condition="'$(Configuration)' != 'Debug'">All</PrivateAssets>
+    </PackageReference>
+  </ItemGroup>
+
+  <ItemGroup>
+    <ProjectReference Include="..\CellSimulation\CellSimulation.csproj" />
+  </ItemGroup>
+</Project>

CellSimulation.Desktop/Program.cs

@@ -0,0 +1,21 @@
+using System;
+using Avalonia;
+
+namespace CellSimulation.Desktop;
+
+sealed class Program
+{
+    // Initialization code. Don't use any Avalonia, third-party APIs or any
+    // SynchronizationContext-reliant code before AppMain is called: things aren't initialized
+    // yet and stuff might break.
+    [STAThread]
+    public static void Main(string[] args) => BuildAvaloniaApp()
+        .StartWithClassicDesktopLifetime(args);
+
+    // Avalonia configuration, don't remove; also used by visual designer.
+    public static AppBuilder BuildAvaloniaApp()
+        => AppBuilder.Configure<App>()
+            .UsePlatformDetect()
+            .WithInterFont()
+            .LogToTrace();
+}

CellSimulation.Desktop/app.manifest

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="utf-8"?>
+<assembly manifestVersion="1.0" xmlns="urn:schemas-microsoft-com:asm.v1">
+  <!-- This manifest is used on Windows only.
+       Don't remove it as it might cause problems with window transparency and embedded controls.
+       For more details visit https://learn.microsoft.com/en-us/windows/win32/sbscs/application-manifests -->
+  <assemblyIdentity version="1.0.0.0" name="CellSimulation.Desktop"/>
+
+  <compatibility xmlns="urn:schemas-microsoft-com:compatibility.v1">
+    <application>
+      <!-- A list of the Windows versions that this application has been tested on
+           and is designed to work with. Uncomment the appropriate elements
+           and Windows will automatically select the most compatible environment. -->
+
+      <!-- Windows 10 -->
+      <supportedOS Id="{8e0f7a12-bfb3-4fe8-b9a5-48fd50a15a9a}" />
+    </application>
+  </compatibility>
+</assembly>

CellSimulation.sln

@@ -0,0 +1,42 @@
+
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio Version 17
+VisualStudioVersion = 17.3.32811.315
+MinimumVisualStudioVersion = 10.0.40219.1
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "CellSimulation", "CellSimulation\CellSimulation.csproj", "{EBFA8512-1EA5-4D8C-B4AC-AB5B48A6D568}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "CellSimulation.Desktop", "CellSimulation.Desktop\CellSimulation.Desktop.csproj", "{ABC31E74-02FF-46EB-B3B2-4E6AE43B456C}"
+EndProject
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution Items", "{3DA99C4E-89E3-4049-9C22-0A7EC60D83D8}"
+	ProjectSection(SolutionItems) = preProject
+		Directory.Packages.props = Directory.Packages.props
+	EndProjectSection
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "BaseCellSimulation", "BaseCellSimulation\BaseCellSimulation.csproj", "{7C692F24-01D5-47FB-957D-94E170351A05}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Any CPU = Debug|Any CPU
+		Release|Any CPU = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{EBFA8512-1EA5-4D8C-B4AC-AB5B48A6D568}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{EBFA8512-1EA5-4D8C-B4AC-AB5B48A6D568}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{EBFA8512-1EA5-4D8C-B4AC-AB5B48A6D568}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{EBFA8512-1EA5-4D8C-B4AC-AB5B48A6D568}.Release|Any CPU.Build.0 = Release|Any CPU
+		{ABC31E74-02FF-46EB-B3B2-4E6AE43B456C}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{ABC31E74-02FF-46EB-B3B2-4E6AE43B456C}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{ABC31E74-02FF-46EB-B3B2-4E6AE43B456C}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{ABC31E74-02FF-46EB-B3B2-4E6AE43B456C}.Release|Any CPU.Build.0 = Release|Any CPU
+		{7C692F24-01D5-47FB-957D-94E170351A05}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{7C692F24-01D5-47FB-957D-94E170351A05}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{7C692F24-01D5-47FB-957D-94E170351A05}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{7C692F24-01D5-47FB-957D-94E170351A05}.Release|Any CPU.Build.0 = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+	GlobalSection(ExtensibilityGlobals) = postSolution
+		SolutionGuid = {83CB65B8-011F-4ED7-BCD3-A6CFA935EF7E}
+	EndGlobalSection
+EndGlobal

CellSimulation/App.axaml

@@ -0,0 +1,15 @@
+<Application xmlns="https://github.com/avaloniaui"
+             xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
+             xmlns:local="using:CellSimulation"
+             x:Class="CellSimulation.App"
+             RequestedThemeVariant="Default">
+             <!-- "Default" ThemeVariant follows system theme variant. "Dark" or "Light" are other available options. -->
+
+    <Application.DataTemplates>
+        <local:ViewLocator/>
+    </Application.DataTemplates>
+
+    <Application.Styles>
+        <FluentTheme />
+    </Application.Styles>
+</Application>

CellSimulation/App.axaml.cs

@@ -0,0 +1,54 @@
+using Avalonia;
+using Avalonia.Controls.ApplicationLifetimes;
+using Avalonia.Data.Core;
+using Avalonia.Data.Core.Plugins;
+using System.Linq;
+using Avalonia.Markup.Xaml;
+using CellSimulation.ViewModels;
+using CellSimulation.Views;
+
+namespace CellSimulation;
+
+public partial class App : Application
+{
+    public override void Initialize()
+    {
+        AvaloniaXamlLoader.Load(this);
+    }
+
+    public override void OnFrameworkInitializationCompleted()
+    {
+        if (ApplicationLifetime is IClassicDesktopStyleApplicationLifetime desktop)
+        {
+            // Avoid duplicate validations from both Avalonia and the CommunityToolkit. 
+            // More info: https://docs.avaloniaui.net/docs/guides/development-guides/data-validation#manage-validationplugins
+            DisableAvaloniaDataAnnotationValidation();
+            desktop.MainWindow = new MainWindow
+            {
+                DataContext = new MainViewModel()
+            };
+        }
+        else if (ApplicationLifetime is ISingleViewApplicationLifetime singleViewPlatform)
+        {
+            singleViewPlatform.MainView = new MainView
+            {
+                DataContext = new MainViewModel()
+            };
+        }
+
+        base.OnFrameworkInitializationCompleted();
+    }
+
+    private void DisableAvaloniaDataAnnotationValidation()
+    {
+        // Get an array of plugins to remove
+        var dataValidationPluginsToRemove =
+            BindingPlugins.DataValidators.OfType<DataAnnotationsValidationPlugin>().ToArray();
+
+        // remove each entry found
+        foreach (var plugin in dataValidationPluginsToRemove)
+        {
+            BindingPlugins.DataValidators.Remove(plugin);
+        }
+    }
+}

CellSimulation/CellSimulation.csproj

@@ -0,0 +1,29 @@
+<Project Sdk="Microsoft.NET.Sdk">
+  <PropertyGroup>
+    <TargetFramework>net9.0</TargetFramework>
+    <Nullable>enable</Nullable>
+    <LangVersion>latest</LangVersion>
+    <AvaloniaUseCompiledBindingsByDefault>true</AvaloniaUseCompiledBindingsByDefault>
+  </PropertyGroup>
+  
+  <ItemGroup>
+    <AvaloniaResource Include="Assets\**" />
+  </ItemGroup>
+
+  <ItemGroup>
+    <PackageReference Include="Avalonia" />
+    <PackageReference Include="Avalonia.Themes.Fluent" />
+    <PackageReference Include="Avalonia.Fonts.Inter" />
+    <!--Condition below is needed to remove Avalonia.Diagnostics package from build output in Release configuration.-->
+    <PackageReference Include="Avalonia.Diagnostics">
+      <IncludeAssets Condition="'$(Configuration)' != 'Debug'">None</IncludeAssets>
+      <PrivateAssets Condition="'$(Configuration)' != 'Debug'">All</PrivateAssets>
+    </PackageReference>
+    <PackageReference Include="CommunityToolkit.Mvvm" />
+    <PackageReference Include="ScottPlot.Avalonia" />
+  </ItemGroup>
+
+  <ItemGroup>
+    <ProjectReference Include="..\BaseCellSimulation\BaseCellSimulation.csproj" />
+  </ItemGroup>
+</Project>

CellSimulation/ViewLocator.cs

@@ -0,0 +1,30 @@
+using System;
+using Avalonia.Controls;
+using Avalonia.Controls.Templates;
+using CellSimulation.ViewModels;
+
+namespace CellSimulation;
+
+public class ViewLocator : IDataTemplate
+{
+    public Control? Build(object? param)
+    {
+        if (param is null)
+            return null;
+
+        var name = param.GetType().FullName!.Replace("ViewModel", "View", StringComparison.Ordinal);
+        var type = Type.GetType(name);
+
+        if (type != null)
+        {
+            return (Control)Activator.CreateInstance(type)!;
+        }
+
+        return new TextBlock { Text = "Not Found: " + name };
+    }
+
+    public bool Match(object? data)
+    {
+        return data is ViewModelBase;
+    }
+}

CellSimulation/ViewModels/MainViewModel.cs

@@ -0,0 +1,9 @@
+using CommunityToolkit.Mvvm.ComponentModel;
+
+namespace CellSimulation.ViewModels;
+
+public partial class MainViewModel : ViewModelBase
+{
+    [ObservableProperty]
+    private string _greeting = "Welcome to Avalonia!";
+}

CellSimulation/ViewModels/ViewModelBase.cs

@@ -0,0 +1,7 @@
+using CommunityToolkit.Mvvm.ComponentModel;
+
+namespace CellSimulation.ViewModels;
+
+public abstract class ViewModelBase : ObservableObject
+{
+}

CellSimulation/Views/MainView.axaml

@@ -0,0 +1,31 @@
+<UserControl xmlns="https://github.com/avaloniaui"
+             xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
+             xmlns:d="http://schemas.microsoft.com/expression/blend/2008"
+             xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
+             xmlns:vm="clr-namespace:CellSimulation.ViewModels"
+             xmlns:ScottPlot="clr-namespace:ScottPlot.Avalonia;assembly=ScottPlot.Avalonia"
+             mc:Ignorable="d" d:DesignWidth="800" d:DesignHeight="450"
+             x:Class="CellSimulation.Views.MainView"
+             x:DataType="vm:MainViewModel">
+  <Design.DataContext>
+    <!-- This only sets the DataContext for the previewer in an IDE,
+         to set the actual DataContext for runtime, set the DataContext property in code (look at App.axaml.cs) -->
+    <vm:MainViewModel />
+  </Design.DataContext>
+  <Grid>
+      <Grid.ColumnDefinitions>
+        <ColumnDefinition Width="*"></ColumnDefinition>
+        <ColumnDefinition Width="4"></ColumnDefinition>
+        <ColumnDefinition Width="*"></ColumnDefinition>
+      </Grid.ColumnDefinitions>
+      <ScottPlot:AvaPlot Name="CellPlot"/>
+      <GridSplitter Grid.Column="1" Background="Black" ResizeDirection="Columns" MinWidth="0"/>
+      <StackPanel Grid.Column="2" Margin="20">
+		  <TextBlock Margin="0 5">Seconds of Symulation</TextBlock>
+          <NumericUpDown x:Name="SecondInput" Value="4" Minimum="1"></NumericUpDown>
+          <TextBlock Margin="0 5">Second Granularity</TextBlock>
+          <NumericUpDown x:Name="Granularity" Value="0.1" Minimum="0.001" Maximum="0.7"></NumericUpDown>
+          <Button x:Name="Simulate" Click="StartSimulation" Margin="0 5"> Simulate</Button>
+      </StackPanel>
+  </Grid>
+</UserControl>

CellSimulation/Views/MainView.axaml.cs

@@ -0,0 +1,77 @@
+using Avalonia.Controls;
+using BaseCellSimulation;
+using ScottPlot;
+using ScottPlot.Avalonia;
+using System.Collections.Generic;
+
+namespace CellSimulation.Views;
+
+public partial class MainView : UserControl
+{
+    List<cellInfo> cellData = new();
+
+    EnviromentState envState = new()
+    {
+       Glucose = 5.0,      // mM — normaler Blutzuckerwert (~90 mg/dL)
+       Oxygen = 0.2,       // mM — entspricht ca. 5% O2 (physiologischer Bereich)
+       Waste = 0.0,        // mM — initial kein Abfallprodukt
+       Lactate = 1.0,      // mM — basaler Spiegel (wird bei anaerobem Stoffwechsel steigen)
+       Insulin = 0.05,     // µM — basal, kann bei Simulation von Stoffwechselantworten angepasst werden
+       Protons = 0.00004,  // mM — entspricht pH 7.4 (10^-7.4 mol/L)
+       Na = 140.0,         // mM — extrazelluläre Natriumkonzentration
+       K = 4.5,         // mM — extrazelluläre Kaliumkonzentration
+       Ca = 0.0018
+    };
+
+    public MainView()
+    {
+        InitializeComponent();
+
+        
+    }
+
+    private void StartSimulation(object? sender, Avalonia.Interactivity.RoutedEventArgs e)
+    {
+        Cell cell = new();
+
+        cell.EnviromentState = envState;
+
+        decimal? granularity = Granularity.Value;
+
+        decimal? seconds = SecondInput.Value;
+
+        cellData = new();
+
+        for (int i = 0; i < seconds/granularity; i++)
+        {
+            envState.Glucose += 0.01;
+            envState.Oxygen += 0.005;
+            cell.Step((double)granularity);
+            cellData.Add(cell.GetCellInfo());
+        }
+
+        
+        AvaPlot avaPlot = CellPlot;
+        avaPlot.Reset();
+        avaPlot.Plot.Title("Cell Simulation Over Time");
+        avaPlot.Plot.XLabel("Time (s)");
+        avaPlot.Plot.YLabel("Concentration / Amount");
+        var ATP = avaPlot.Plot.Add.Scatter(cellData.ConvertAll(c => c.time).ToArray(), cellData.ConvertAll(c => c.resources["ATP"]).ToArray());
+        ATP.LegendText = "ATP";
+        var Glucose = avaPlot.Plot.Add.Scatter(cellData.ConvertAll(c => c.time).ToArray(), cellData.ConvertAll(c => c.resources["Glucose"]).ToArray());
+        Glucose.LegendText = "Glucose";
+        var NADH = avaPlot.Plot.Add.Scatter(cellData.ConvertAll(c => c.time).ToArray(), cellData.ConvertAll(c => c.resources["NADH"]).ToArray());
+        NADH.LegendText = "NADH";
+        var NAD = avaPlot.Plot.Add.Scatter(cellData.ConvertAll(c => c.time).ToArray(), cellData.ConvertAll(c => c.resources["NAD"]).ToArray());
+        NAD.LegendText = "NAD";
+        var AminoAcids = avaPlot.Plot.Add.Scatter(cellData.ConvertAll(c => c.time).ToArray(), cellData.ConvertAll(c => c.resources["AminoAcids"]).ToArray());
+        AminoAcids.LegendText = "AminoAcids";
+        var CytosolicCa = avaPlot.Plot.Add.Scatter(cellData.ConvertAll(c => c.time).ToArray(), cellData.ConvertAll(c => c.caState.CytosolicCa).ToArray());
+        CytosolicCa.LegendText = "Cytosolic Ca";
+        var ER_Ca = avaPlot.Plot.Add.Scatter(cellData.ConvertAll(c => c.time).ToArray(), cellData.ConvertAll(c => c.caState.ER_Ca).ToArray());
+        ER_Ca.LegendText = "ER Ca";
+        avaPlot.Plot.Legend.Orientation = Orientation.Horizontal;
+        avaPlot.Plot.ShowLegend(Edge.Bottom);
+        avaPlot.Refresh();
+    }
+}

CellSimulation/Views/MainWindow.axaml

@@ -0,0 +1,12 @@
+<Window xmlns="https://github.com/avaloniaui"
+        xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
+        xmlns:vm="using:CellSimulation.ViewModels"
+        xmlns:d="http://schemas.microsoft.com/expression/blend/2008"
+        xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
+        xmlns:views="clr-namespace:CellSimulation.Views"
+        mc:Ignorable="d" d:DesignWidth="800" d:DesignHeight="450"
+        x:Class="CellSimulation.Views.MainWindow"
+        Icon="/Assets/avalonia-logo.ico"
+        Title="CellSimulation">
+        <views:MainView />
+</Window>

CellSimulation/Views/MainWindow.axaml.cs

@@ -0,0 +1,11 @@
+using Avalonia.Controls;
+
+namespace CellSimulation.Views;
+
+public partial class MainWindow : Window
+{
+    public MainWindow()
+    {
+        InitializeComponent();
+    }
+}

Directory.Packages.props

@@ -0,0 +1,21 @@
+<Project>
+  <!-- https://learn.microsoft.com/en-us/nuget/consume-packages/central-package-management -->
+  <PropertyGroup>
+    <ManagePackageVersionsCentrally>true</ManagePackageVersionsCentrally>
+  </PropertyGroup>
+  <ItemGroup>
+    <!-- Avalonia packages -->
+    <!-- Important: keep version in sync! -->
+    <PackageVersion Include="Avalonia" Version="11.3.6" />
+    <PackageVersion Include="Avalonia.Themes.Fluent" Version="11.3.6" />
+    <PackageVersion Include="Avalonia.Fonts.Inter" Version="11.3.6" />
+    <PackageVersion Include="Avalonia.Diagnostics" Version="11.3.6" />
+    <PackageVersion Include="Avalonia.Desktop" Version="11.3.6" />
+    <PackageVersion Include="Avalonia.iOS" Version="11.3.6" />
+    <PackageVersion Include="Avalonia.Browser" Version="11.3.6" />
+    <PackageVersion Include="Avalonia.Android" Version="11.3.6" />
+    <PackageVersion Include="CommunityToolkit.Mvvm" Version="8.4.0" />
+    <PackageVersion Include="ScottPlot.Avalonia" Version="5.1.57" />
+    <PackageVersion Include="Xamarin.AndroidX.Core.SplashScreen" Version="1.0.1.15" />
+  </ItemGroup>
+</Project>