From 7af03a10070deec24a46f2fb0887b74563e021dc Mon Sep 17 00:00:00 2001 From: "Cody, Jonathan William" Date: Mon, 27 Jun 2022 20:39:41 -0400 Subject: [PATCH] Add files via upload --- ICsolvers/N803_single.m | 42 ++++++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/ICsolvers/N803_single.m b/ICsolvers/N803_single.m index d8b7188..671123d 100644 --- a/ICsolvers/N803_single.m +++ b/ICsolvers/N803_single.m @@ -8,12 +8,12 @@ % | Pienaar Computational Systems Pharmacology Lab | % \--------------------------------------------------------------/ % -% Nomenclature: V = SIV virions [#/ç„¡] -% T8 = total CD8+ T cells [#/ç„¡] -% E0 = resting SIV-specific CD8+ T cells [#/ç„¡] -% Ea = active SIV-specific CD8+ T cells [#/ç„¡] -% B0 = resting bystander CD8+ T cells [#/ç„¡] -% Ba = active bystander CD8+ T cells [#/ç„¡] +% Nomenclature: V = SIV virions [#/µL] +% T8 = total CD8+ T cells [#/µL] +% E0 = resting SIV-specific CD8+ T cells [#/µL] +% Ea = active SIV-specific CD8+ T cells [#/µL] +% B0 = resting bystander CD8+ T cells [#/µL] +% Ba = active bystander CD8+ T cells [#/µL] % X = N803 at absorption site [pmol/kg] % C = N803 plasma concentration [pM] % R = regulation [] (dimensionless quantity) @@ -52,7 +52,7 @@ % Rename inputed parameters ----------------------------------------------- Vi = AllPars(01) ;% V initial value [log(#/mL)] -EBi = AllPars(02) ;% E+B initial value [#/ç„¡] +EBi = AllPars(02) ;% E+B initial value [#/µL] fE = AllPars(03) ;% initial frequency: E/(E+B) fEA = AllPars(04) ;% initial frequency: Ea/E q = AllPars(05) ;% V growth rate (if E+B were absent) [/d] @@ -61,7 +61,7 @@ V50B = AllPars(08) ;% 50% viral stimulation saturation for B [#/mL] mEn = AllPars(09) ;% normalized Ea reversion rate constant [] mBn = AllPars(10) ;% normalized Ba reversion rate constant [] -EB50 = AllPars(11) ;% 50% E+B proliferation saturation [#/ç„¡] +EB50 = AllPars(11) ;% 50% E+B proliferation saturation [#/µL] pE = AllPars(12) ;% Ea proliferation rate constant [/d] pB = AllPars(13) ;% Ba proliferation rate constant [/d] d = AllPars(14) ;% E0/B0 death rate constant [/d] @@ -70,11 +70,11 @@ ka = AllPars(17) ;% N803 absorption rate constant [/d] ke = AllPars(18) ;% N803 elimination rate constant [/d] vd = AllPars(19) ;% N803 'volume of distribution'/'bioavailability' [L/kg] -C50 = AllPars(20) ;% 50% N803 stimulation concentration [pM] (Cohort 1) +C50 = AllPars(20) ;% 50% N803 stimulation concentration [pM] pm = AllPars(21) ;% E0/B0 maximum proliferation rate [] aE1 = AllPars(22) ;% E activation stimulation factor [] aB1 = AllPars(23) ;% B activation stimulation factor [] -sig = AllPars(24) ;% sB/sE regulation generation rate ratio [/d] +sig = AllPars(24) ;% sB/sE regulation generation rate ratio dR = AllPars(25) ;% R decay rate constant [/d] gE2 = AllPars(26) ;% initial E killing regulation [] gB2 = AllPars(27) ;% initial B killing regulation [] @@ -85,9 +85,9 @@ %% ------------------------------------------------------------------------ % Calculate some initial conditions & parameters -------------------------- -Vi = 10^(Vi-3) ;% V initial value [#/ç„¡] -V50E = V50E/1000 ;% 50% viral stimulation saturation for E [#/ç„¡] -V50B = V50B/1000 ;% 50% viral stimulation saturation for B [#/ç„¡] +Vi = 10^(Vi-3) ;% V initial value [#/µL] +V50E = V50E/1000 ;% 50% viral stimulation saturation for E [#/µL] +V50B = V50B/1000 ;% 50% viral stimulation saturation for B [#/µL] % restrict mE and mB such that initial activation aE and aB are positive UE = (2*pE/(pE+dA))^7 ; @@ -139,8 +139,8 @@ p0 = pi * (EB50+EBi)/EB50 * (1+p2) ;% E0/B0 proliferation rate con [/d] p1 = pm/p0 ;% E0/B0 proliferation stimulation factor -gE0 = q / ( EA/(1+gE2) + psi*BA/(1+gB2) ) ;% Ea killing rate con [ç„¡/#-d] -gB0 = psi*gE0 ;% Ba killing rate constant [ç„¡/#-d] +gE0 = q / ( EA/(1+gE2) + psi*BA/(1+gB2) ) ;% Ea killing rate con [µL/#-d] +gB0 = psi*gE0 ;% Ba killing rate constant [µL/#-d] sE = dR / ( Vi/(V50E+Vi) + sig*Vi/(V50B+Vi) ) ;% regulation gen by E act sB = sig*sE ;% regulation generation by B activation @@ -149,17 +149,17 @@ % Prepare parameter and initial value vectors and call 'N803_model_2' ----- Pars(01) = q ;% V growth rate (if E+B were absent) [/d] -Pars(02) = gE0 ;% Ea killing rate constant [ç„¡/#-d] -Pars(03) = gB0 ;% Ba killing rate constant [ç„¡/#-d] +Pars(02) = gE0 ;% Ea killing rate constant [µL/#-d] +Pars(03) = gB0 ;% Ba killing rate constant [µL/#-d] -Pars(04) = V50E ;% 50% viral stimulation saturation for E [#/ç„¡] -Pars(05) = V50B ;% 50% viral stimulation saturation for B [#/ç„¡] +Pars(04) = V50E ;% 50% viral stimulation saturation for E [#/µL] +Pars(05) = V50B ;% 50% viral stimulation saturation for B [#/µL] Pars(06) = aE0 ;% E0 activation rate constant [/d] Pars(07) = aB0 ;% B0 activation rate constant [/d] Pars(08) = mE ;% Ea reversion rate constant [/d] Pars(09) = mB ;% Ba reversion rate constant [/d] -Pars(10) = EB50 ;% 50% E+B proliferation saturation [#/ç„¡] +Pars(10) = EB50 ;% 50% E+B proliferation saturation [#/µL] Pars(11) = p0 ;% E0/B0 proliferation rate constant [/d] Pars(12) = pE ;% Ea proliferation rate constant [/d] Pars(13) = pB ;% Ba proliferation rate constant [/d] @@ -193,4 +193,4 @@ Y_OUT = N803_model_2(SoluTimes,DoseTimes,Pars,Yic,varargin) ; -end +end \ No newline at end of file