Initial commit adding project files for Matlab and python

.gitignore

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+.vscode
+
+# MATLAB files
+*.mex*
+*.asv
+*/*/ess_report.mat
+*/ess_report.mat
+Matlab/**/Results
+Matlab/**/Results_PI
+Matlab/**/Results_PPL
+Matlab/setup.m
+parfor_done.tmp
+Matlab/Figures/*.png
+Matlab/Figures/PI-waterfall/*.pdf
+Matlab/Log
+Matlab/slurm*.out
+
+# Python files
+python/results/
+python/figures
+Pipfile
+__pycache__

Matlab/Models/AlcoholModel.txt

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+********** MODEL NAME
+AlcoholModel
+
+********** MODEL NOTES
+
+********** MODEL STATES 
+d/dt(Vol_Stomach) = + vol_drink_per_time*10 - r2            % dL
+d/dt(Kcal_Liquid) = + vol_drink_per_time*kcal_liquid_per_vol - rKcal_clearance       % kcal [ L * kcal/L = kcal]
+
+d/dt(max_Kcal_Solid) = 0
+d/dt(Kcal_Solid) = -r_Kcal_Solid
+d/dt(time_elapsed) = 1
+
+d/dt(EtOH_Pool) = + r_poolIn*Vol_Stomach - r_poolOut                    %mg
+
+d/dt(Conc_EtOH_Stomach)  =  r_drinkEtOH  - r_poolIn + r_poolOut/Vol_Stomach % mg/dL
+d/dt(Mass_EtOH_Intestines) = + r2*Conc_EtOH_Stomach - r3  - r4          % mg
+
+d/dt(Blood_Conc) =  + (r3/V_Blood) - r5*(V_Liver/V_Blood)               %mg/dL 
+
+d/dt(Plasma_acetate) = + r5 - r6                  %mg/dL  
+
+d/dt(PEth) = rPEth - rPEth_bound + rPEth_release - rPEth_clearance 
+d/dt(PEth_Bound) =  rPEth_bound - rPEth_release
+
+
+Vol_Stomach(0) = 0.001
+Kcal_Liquid(0) = 0
+max_Kcal_Solid(0) = 0
+Kcal_Solid(0) = 0
+time_elapsed(0) = 0
+EtOH_Pool(0) = 0
+Conc_EtOH_Stomach(0) = 0
+Mass_EtOH_Intestines(0) = 0
+Blood_Conc(0)=0
+Plasma_acetate(0) = 0
+PEth(0) = 0
+PEth_Bound(0) = 0
+
+********** MODEL PARAMETERS
+kPEth = 1
+kPEth_out = 1
+kPEth_bind = 1
+kPEth_release = 1
+
+k_poolIn = 1
+k_poolOut = 1
+
+Vmax = 1
+km  = 1
+k_kcal = 1
+
+k3  = 1
+k4  = 0.5 
+
+k6 = 1
+
+VmaxADH    = 1
+VmaxCYP2E1 = 1
+
+KmADH     = 1 % based on literature values 
+KmCYP2E1  = 1 % based on literature values 
+
+k_Kcal_clearance = 1
+
+% Constant Inputs 
+EtOH_conc=0
+vol_drink_per_time = 0
+kcal_liquid_per_vol = 0
+
+sex = 1 % male=1 , female=0
+weight = 104 % Kg
+height = 1.85 % m
+
+********** MODEL VARIABLES
+SS_vol = 0.001
+
+V_Liver = 15
+V_Blood = ((1-sex)*(0.3561 * height^3 + 0.03308 * weight + 0.1833) + sex*(0.3669 * height^3 + 0.03219 * weight + 0.6041))*10 % dL     Nadler's Equation for total blood volume
+
+conc_drink = EtOH_conc*789.1    %mg/dL
+
+vADH = (VmaxADH*Blood_Conc/( KmADH + Blood_Conc))           
+vCYP2E1 = (VmaxCYP2E1*Blood_Conc/( KmCYP2E1 + Blood_Conc))  
+
+kcal_solid_vol = max(1,Kcal_Solid)/(4*100) % 4kcal/g assumes 1g/ml, 100 scales ml--> dL 
+
+%measurables
+yEtOH = Blood_Conc   % mg/dL
+yAcetate = Plasma_acetate*(1/10.2)                              %mg/dL --> mM
+yBrAC = ( 0.840*(Blood_Conc/1000) + 0.00367 )    % [g/210L * 1/210 * 2100 = g/L * 2100 = g/L * scale] % 10 cause Blood_Conc is in /dL and needs tobe scaled up to /L
+yPEth = PEth
+yGastricVolume = Vol_Stomach 
+yKcalLiquid = Kcal_Liquid 
+
+********** MODEL REACTIONS
+r2 = Vmax*( (Vol_Stomach-SS_vol)/((Vol_Stomach-SS_vol) + km) ) * exp( - max(0, Kcal_Liquid)/k_kcal )
+
+r_Kcal_Solid = (max_Kcal_Solid * 1.88 * 0.010* (0.010*max(0, time_elapsed))^0.86  * exp(-(0.010*max(0, time_elapsed))^1.86)) 
+
+r_poolIn  = gt(Vol_Stomach, 2*SS_vol) * gt(Kcal_Solid, 1) * max(0, (Conc_EtOH_Stomach - EtOH_Pool/kcal_solid_vol) * k_poolIn)
+r_poolOut =  gt(Vol_Stomach, 2*SS_vol) * gt(Kcal_Solid, 1) * EtOH_Pool * k_poolOut
+
+r_drinkEtOH = (conc_drink - Conc_EtOH_Stomach )*(vol_drink_per_time*10/Vol_Stomach)
+rKcal_clearance = Kcal_Liquid*k_Kcal_clearance
+
+r3 = max(0, Mass_EtOH_Intestines*k3) 
+r4 = Mass_EtOH_Intestines*k4
+
+r5  = vADH + vCYP2E1
+
+r6 = Plasma_acetate*k6
+
+rPEth = kPEth*Blood_Conc
+rPEth_clearance = kPEth_out*PEth
+rPEth_bound = kPEth_bind*PEth
+rPEth_release = max(0, kPEth_release*( PEth_Bound - PEth ))
+
+********** MODEL FUNCTIONS
+********** MODEL EVENTS
+event1 = le(Kcal_Solid, 0), Kcal_Solid, 0, max_Kcal_Solid, 0, EtOH_Pool, 0
+********** MODEL MATLAB FUNCTIONS

Matlab/Models/AlcoholModel_FoodH2.txt

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+********** MODEL NAME
+AlcoholModel_FoodH2
+
+********** MODEL NOTES
+
+********** MODEL STATES 
+d/dt(Vol_Stomach) = + vol_drink_per_time*10 - r2            % dL
+d/dt(Kcal_Liquid) = + vol_drink_per_time*kcal_liquid_per_vol - rKcal_clearance       % kcal [ L * kcal/L = kcal]
+
+d/dt(max_Kcal_Solid) = 0
+d/dt(Kcal_Solid) = -r_Kcal_Solid
+d/dt(time_elapsed) = 1
+
+d/dt(Conc_EtOH_Stomach)  =  r_drinkEtOH  % mg/dL
+d/dt(Mass_EtOH_Intestines) = + r2*Conc_EtOH_Stomach - r3  - r4          % mg
+
+d/dt(Blood_Conc) =  + (r3/V_Blood) - r5*(V_Liver/V_Blood)               %mg/dL 
+
+d/dt(Plasma_acetate) = + r5 - r6                  %mg/dL  
+
+d/dt(PEth) = rPEth - rPEth_bound + rPEth_release - rPEth_clearance 
+d/dt(PEth_Bound) =  rPEth_bound - rPEth_release
+
+
+Vol_Stomach(0) = 0.001
+Kcal_Liquid(0) = 0
+max_Kcal_Solid(0) = 0
+Kcal_Solid(0) = 0
+time_elapsed(0) = 0
+Conc_EtOH_Stomach(0) = 0
+Mass_EtOH_Intestines(0) = 0
+Blood_Conc(0)=0
+Plasma_acetate(0) = 0
+PEth(0) = 0
+PEth_Bound(0) = 0
+
+********** MODEL PARAMETERS
+kPEth = 1
+kPEth_out = 1
+kPEth_bind = 1
+kPEth_release = 1
+
+k_foodBlock = 1
+
+Vmax = 1
+km  = 1
+k_kcal = 1
+
+k3  = 1
+k4  = 0.5 
+
+k6 = 1
+
+VmaxADH    = 1
+VmaxCYP2E1 = 1
+
+KmADH     = 1 % based on literature values 
+KmCYP2E1  = 1 % based on literature values 
+
+k_Kcal_clearance = 1
+
+% Constant Inputs 
+EtOH_conc=0
+vol_drink_per_time = 0
+kcal_liquid_per_vol = 0
+
+sex = 1 % male=1 , female=0
+weight = 104 % Kg
+height = 1.85 % m
+
+********** MODEL VARIABLES
+SS_vol = 0.001
+
+V_Liver = 15
+V_Blood = ((1-sex)*(0.3561 * height^3 + 0.03308 * weight + 0.1833) + sex*(0.3669 * height^3 + 0.03219 * weight + 0.6041))*10 % dL     Nadler's Equation for total blood volume
+
+conc_drink = EtOH_conc*789.1    %mg/dL
+
+vADH = (VmaxADH*Blood_Conc/( KmADH + Blood_Conc))           
+vCYP2E1 = (VmaxCYP2E1*Blood_Conc/( KmCYP2E1 + Blood_Conc))  
+
+kcal_solid_vol = max(1,Kcal_Solid)/(4*100) % 4kcal/g assumes 1g/ml, 100 scales ml--> dL 
+
+%measurables
+yEtOH = Blood_Conc   % mg/dL
+yAcetate = Plasma_acetate*(1/10.2)                              %mg/dL --> mM
+yBrAC = ( 0.840*(Blood_Conc/1000) + 0.00367 )    % [g/210L * 1/210 * 2100 = g/L * 2100 = g/L * scale] % 10 cause Blood_Conc is in /dL and needs tobe scaled up to /L
+yPEth = PEth
+yGastricVolume = Vol_Stomach 
+yKcalLiquid = Kcal_Liquid 
+
+********** MODEL REACTIONS
+r2 = Vmax*( (Vol_Stomach-SS_vol)/((Vol_Stomach-SS_vol) + km) ) * exp( - max(0, Kcal_Liquid)/k_kcal ) * (1/(1 + k_foodBlock*Kcal_Solid))
+
+r_Kcal_Solid = (max_Kcal_Solid * 1.88 * 0.010* (0.010*max(0, time_elapsed))^0.86  * exp(-(0.010*max(0, time_elapsed))^1.86))    % doi: 10.1016/S0002-9270(00)00868-6
+
+r_drinkEtOH = (conc_drink - Conc_EtOH_Stomach )*(vol_drink_per_time*10/Vol_Stomach)
+rKcal_clearance = Kcal_Liquid*k_Kcal_clearance
+
+r3 = max(0, Mass_EtOH_Intestines*k3) 
+r4 = Mass_EtOH_Intestines*k4
+
+r5  = vADH + vCYP2E1
+
+r6 = Plasma_acetate*k6
+
+rPEth = kPEth*Blood_Conc
+rPEth_clearance = kPEth_out*PEth
+rPEth_bound = kPEth_bind*PEth
+rPEth_release = max(0, kPEth_release*( PEth_Bound - PEth ))
+
+********** MODEL FUNCTIONS
+********** MODEL EVENTS
+event1 = le(Kcal_Solid, 0), Kcal_Solid, 0, max_Kcal_Solid, 0
+********** MODEL MATLAB FUNCTIONS

Matlab/Models/AlcoholModel_FoodH3.txt

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+********** MODEL NAME
+AlcoholModel_FoodH3
+
+********** MODEL NOTES
+
+********** MODEL STATES 
+d/dt(Vol_Stomach) = + vol_drink_per_time*10 - r2            % dL
+d/dt(Kcal_Liquid) = + vol_drink_per_time*kcal_liquid_per_vol - rKcal_clearance       % kcal [ L * kcal/L = kcal]
+
+d/dt(max_Kcal_Solid) = 0
+d/dt(Kcal_Solid) = -r_Kcal_Solid
+d/dt(time_elapsed) = 1
+
+d/dt(Conc_EtOH_Stomach)  =  r_drinkEtOH  - r_gastricADH % mg/dL
+d/dt(Mass_EtOH_Intestines) = + r2*Conc_EtOH_Stomach - r3  - r4          % mg
+
+d/dt(Blood_Conc) =  + (r3/V_Blood) - r5*(V_Liver/V_Blood)               %mg/dL 
+
+d/dt(Plasma_acetate) = + r5 - r6                  %mg/dL  
+
+d/dt(PEth) = rPEth - rPEth_bound + rPEth_release - rPEth_clearance 
+d/dt(PEth_Bound) =  rPEth_bound - rPEth_release
+
+Vol_Stomach(0) = 0.001
+Kcal_Liquid(0) = 0
+max_Kcal_Solid(0) = 0
+Kcal_Solid(0) = 0
+time_elapsed(0) = 0
+Conc_EtOH_Stomach(0) = 0
+Mass_EtOH_Intestines(0) = 0
+Blood_Conc(0)=0
+Plasma_acetate(0) = 0
+PEth(0) = 0
+PEth_Bound(0) = 0
+
+********** MODEL PARAMETERS
+kPEth = 1
+kPEth_out = 1
+kPEth_bind = 1
+kPEth_release = 1
+
+VmaxGastricADH = 1
+k_foodBlock = 1
+
+Vmax = 1
+km  = 1
+k_kcal = 1
+
+k3  = 1
+k4  = 0.5 
+
+k6 = 1
+
+VmaxADH    = 1
+VmaxCYP2E1 = 1
+
+KmADH     = 1 % based on literature values 
+KmCYP2E1  = 1 % based on literature values 
+
+k_Kcal_clearance = 1
+
+% Constant Inputs 
+EtOH_conc=0
+vol_drink_per_time = 0
+kcal_liquid_per_vol = 0
+
+sex = 1 % male=1 , female=0
+weight = 104 % Kg
+height = 1.85 % m
+
+********** MODEL VARIABLES
+SS_vol = 0.001
+
+V_Liver = 15
+V_Blood = ((1-sex)*(0.3561 * height^3 + 0.03308 * weight + 0.1833) + sex*(0.3669 * height^3 + 0.03219 * weight + 0.6041))*10 % dL     Nadler's Equation for total blood volume
+
+conc_drink = EtOH_conc*789.1    %mg/dL
+
+vADH = (VmaxADH*Blood_Conc/( KmADH + Blood_Conc))           
+vCYP2E1 = (VmaxCYP2E1*Blood_Conc/( KmCYP2E1 + Blood_Conc))  
+
+kcal_solid_vol = max(1,Kcal_Solid)/(4*100) % 4kcal/g assumes 1g/ml, 100 scales ml--> dL 
+
+%measurables
+yEtOH = Blood_Conc   % mg/dL
+yAcetate = Plasma_acetate*(1/10.2)                              %mg/dL --> mM
+yBrAC = ( 0.840*(Blood_Conc/1000) + 0.00367 )    % [g/210L * 1/210 * 2100 = g/L * 2100 = g/L * scale] % 10 cause Blood_Conc is in /dL and needs tobe scaled up to /L
+yPEth = PEth
+yGastricVolume = Vol_Stomach 
+yKcalLiquid = Kcal_Liquid 
+
+********** MODEL REACTIONS
+r2 = Vmax*( (Vol_Stomach-SS_vol)/((Vol_Stomach-SS_vol) + km) ) * exp( - max(0, Kcal_Liquid)/k_kcal ) * (1/(1 + k_foodBlock*Kcal_Solid))
+
+r_Kcal_Solid = (max_Kcal_Solid * 1.88 * 0.010* (0.010*max(0, time_elapsed))^0.86  * exp(-(0.010*max(0, time_elapsed))^1.86))    % doi: 10.1016/S0002-9270(00)00868-6
+
+r_drinkEtOH = (conc_drink - Conc_EtOH_Stomach )*(vol_drink_per_time*10/Vol_Stomach)
+rKcal_clearance = Kcal_Liquid*k_Kcal_clearance
+
+r_gastricADH = VmaxGastricADH*(Conc_EtOH_Stomach/(KmADH + Conc_EtOH_Stomach))
+
+r3 = max(0, Mass_EtOH_Intestines*k3) 
+r4 = Mass_EtOH_Intestines*k4
+
+r5  = vADH + vCYP2E1
+
+r6 = Plasma_acetate*k6
+
+rPEth = kPEth*Blood_Conc
+rPEth_clearance = kPEth_out*PEth
+rPEth_bound = kPEth_bind*PEth
+rPEth_release = max(0, kPEth_release*( PEth_Bound - PEth ))
+
+********** MODEL FUNCTIONS
+********** MODEL EVENTS
+event1 = le(Kcal_Solid, 0), Kcal_Solid, 0, max_Kcal_Solid, 0
+********** MODEL MATLAB FUNCTIONS