From 7488105f4592baa5c3d1e865db052eae077429c5 Mon Sep 17 00:00:00 2001 From: "Cody, Jonathan William" Date: Mon, 24 Jan 2022 13:56:34 -0500 Subject: [PATCH] Add files via upload --- N803_model_2.m | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/N803_model_2.m b/N803_model_2.m index 36a425c..6410fd4 100644 --- a/N803_model_2.m +++ b/N803_model_2.m @@ -1,14 +1,14 @@ %% N803_model_2.m - solves ODE model for N-803 treatment of SIV % % /--------------------------------------------------------------\ -% | Date: 10/28/2021 | +% | Date: 10/31/2021 | % | Author: Jonathan Cody | % | Affiliation: Purdue University | % | Weldon School of Biomedical Engineering | % | Pienaar Computational Systems Pharmacology Lab | % \--------------------------------------------------------------/ % -% Version 2D+ +% Version 2D+ (also allowing regulation calibration) % % Nomenclature: V = SIV virions [#/µL] % E0 = resting SIV-specific CD8+ T cells [#/µL] @@ -54,6 +54,7 @@ % % Y_OUT(:,1) = V at points in 'SoluTimes' [log fold change] % Y_OUT(:,2) = E at points in 'SoluTimes' [fold change] +% Y_OUT(:,3) = R at points in 'SoluTimes' [fold change] % % If 'fullOut' is non-empty, more columns are included (see code) % @@ -190,9 +191,9 @@ Y = abs(Y) ;% removing negatives resulting from numerical error -% V,E,K [fold change] Y_OUT = [ log10(Y(:,1)/Vi) ... V [log fold change] - , sum(Y(:,2:13),2)/EBi ];% E [fold change] + , sum(Y(:,2:13),2)/EBi ... E [fold change] + , Y(:,15+nR)/Y(1,15+nR) ];% R [fold change] %% ------------------------------------------------------------------------ % Add columns to 'Y_OUT' (if requested) ----------------------------------- @@ -208,19 +209,18 @@ R = Y(:,15+nR) ;% immune regulation [] [F,T] = terms(Y) ;% modifiers for 'gE0','gB0','p0','aE0','aB0' -Y_OUT(:,03) = (E0+Ea) / (E0(1)+Ea(1)) ;% E [fold change] -Y_OUT(:,04) = (B0+Ba) / (B0(1)+Ba(1)) ;% B [fold change] -Y_OUT(:,05) = E0 / E0(1) ;% E0 [fold change] -Y_OUT(:,06) = B0 / B0(1) ;% B0 [fold change] -Y_OUT(:,07) = Ea / Ea(1) ;% Ea [fold change] -Y_OUT(:,08) = Ba / Ba(1) ;% Ba [fold change] -Y_OUT(:,09) = (E0+Ea)./(E0+B0+Ea+Ba) ;% E frequency in (E+B) -Y_OUT(:,10) = (Ea+Ba)./(E0+B0+Ea+Ba) ;% activated frequency in (E+B) -Y_OUT(:,11) = (Ea)./(E0+Ea) ;% activated frequency in E -Y_OUT(:,12) = (Ba)./(B0+Ba) ;% activated frequency in B -Y_OUT(:,13) = Y(:,14) ;% X [pmol/kg] -Y_OUT(:,14) = Y(:,15) ;% C [pM] -Y_OUT(:,15) = R / R(1) ;% R [fold change] +Y_OUT(:,04) = (E0+Ea) / (E0(1)+Ea(1)) ;% E [fold change] +Y_OUT(:,05) = (B0+Ba) / (B0(1)+Ba(1)) ;% B [fold change] +Y_OUT(:,06) = E0 / E0(1) ;% E0 [fold change] +Y_OUT(:,07) = B0 / B0(1) ;% B0 [fold change] +Y_OUT(:,08) = Ea / Ea(1) ;% Ea [fold change] +Y_OUT(:,09) = Ba / Ba(1) ;% Ba [fold change] +Y_OUT(:,10) = (E0+Ea)./(E0+B0+Ea+Ba) ;% E frequency in (E+B) +Y_OUT(:,11) = (Ea+Ba)./(E0+B0+Ea+Ba) ;% activated frequency in (E+B) +Y_OUT(:,12) = (Ea)./(E0+Ea) ;% activated frequency in E +Y_OUT(:,13) = (Ba)./(B0+Ba) ;% activated frequency in B +Y_OUT(:,14) = Y(:,14) ;% X [pmol/kg] +Y_OUT(:,15) = Y(:,15) ;% C [pM] Y_OUT(:,16) = T ;% T [] Y_OUT(:,17) = F(:,01) ;% N803 effect [] @@ -305,7 +305,7 @@ dY(4:9)= 2*pE*Ea(1:6) - dA*Ea(2:7) - pE*Ea(2:7) ;% dE2-7/dt dY(10) = 2*pE*Ea(7) - dA*Ea(8) - mE*Ea(8) ;% dE8/dt dY(11) = p*B0 - aB*B0 - d*B0 + mB*Ba(2) ;% dB0/dt - dY(12) = + aB*B0 - dA*Ba(2) - pB*Ba(1) ;% dB1/dt + dY(12) = + aB*B0 - dA*Ba(2) - pB*Ba(1) ;% dB1/dt !!!!! dA*Ba(1) !!!!! dY(13) = 2*pB*Ba(1) - dA*Ba(2) - mB*Ba(2) ;% dB2/dt dY(14) = - ka*X ;% dX/dt dY(15) = ka*X/vd - ke*C ;% dC/dt