From 80132413abe40a35ad1142d75251ae0459bf0f0b Mon Sep 17 00:00:00 2001 From: "Cody, Jonathan William" Date: Sun, 25 Dec 2022 08:59:35 -0600 Subject: [PATCH] Delete HIV_acute_V1.m --- Legacy Code/HIV_acute_V1.m | 117 ------------------------------------- 1 file changed, 117 deletions(-) delete mode 100644 Legacy Code/HIV_acute_V1.m diff --git a/Legacy Code/HIV_acute_V1.m b/Legacy Code/HIV_acute_V1.m deleted file mode 100644 index 830e774..0000000 --- a/Legacy Code/HIV_acute_V1.m +++ /dev/null @@ -1,117 +0,0 @@ -function Yout = HIV_acute_V1(t,~,P,~) -% -% /-------------------------------------------------------\ -% | Date: 3/5/2018 | -% | Author: Jonathan Cody | -% | Institution: Purdue University | -% | Weldon School of Biomedical Engineering | -% | Pienaar Lab | -% \-------------------------------------------------------/ -% -% Solves host-level acute-phase model V.1 for ALT-803 project -% -% Nomenclature: T4 = target CD4+ T cell -% TI = infected CD4+ T cell -% T8 = resting CD8+ T cell -% TC = activated CD8+ T cell -% K = natural killer cell -% V = virion concentration -% DC = antigen presenting dendritic cell (not modeled) -% -% INPUTS ================================================================== -% -% t = time points at which to evaluate solution [day] (inc. initial time) -% ~ = not used (input anything) -% P = parameter vector corresponding to the following list: -% -% R(:,1) = [X X] ;% T4 initial concentration [#/ul] -% R(:,2) = [X X] ;% T8 initial concentration [#/ul] -% R(:,3) = [X X] ;% K initial concentration [#/ul] -% R(:,4) = [X X] ;% V initial concentration [log(#/ml)] -% R(:,5) = [X X] ;% T4 decay rate constant [/day] -% R(:,6) = [X X] ;% TI decay rate constant proportionality [] (see calcs) -% R(:,7) = [X X] ;% T8 decay rate constant [/day] -% R(:,8) = [X X] ;% TC decay rate constant proportionality [] (see calcs) -% R(:,9) = [X X] ;% K decay rate constant [/day] -% R(:,10) = [X X] ;% V decay rate constant [/day] -% R(:,11) = [X X] ;% V production by TI rate constant [/day] -% R(:,12) = [X X] ;% T4 infection rate constant [ul/#-day] -% R(:,13) = [X X] ;% T8 activation by DC rate constant [ul/#-day] -% R(:,14) = [X X] ;% TI killing by TC rate constant [ul/#-day] -% R(:,15) = [X X] ;% TI killing by K rate constant [ul/#-day] -% R(:,16) = [X X] ;% TC proliferation by DC saturated rate constant [/day] -% R(:,17) = [X X] ;% K proliferation by DC saturated rate constant [/day] -% R(:,18) = [X X] ;% TC proliferation by DC half-sat. concentration [#/ul] -% R(:,19) = [X X] ;% K proliferation by DC half-sat. concentration [#/ul] -% -% OUTPUTS ================================================================= -% -% Omit the fourth input to output the following: -% Yout(:,1) = V concentration at each time point in 't' [log(#/ml)] -% Yout(:,2) = T4+TI concentration at each time point in 't' [#/ul] -% Yout(:,3) = T8+TC concentration at each time point in 't' [#/ul] -% Yout(:,4) = K concentration at each time point in 't' [#/ul] -% -% Include a fourth input (anything) to output the following: -% Yout(:,1) = T4 concentration at each time point in 't' [#/ul] -% Yout(:,2) = TI concentration at each time point in 't' [#/ul] -% Yout(:,3) = T8 concentration at each time point in 't' [#/ul] -% Yout(:,4) = TC concentration at each time point in 't' [#/ul] -% Yout(:,5) = K concentration at each time point in 't' [#/ul] -% Yout(:,6) = V concentration at each time point in 't' [log(#/ml)] - -% CALCULATIONS ============================================================ - -% generating constants ---------------------------------------------------- - -P(4) = (10.^P(4))/1e3 ;% converting V initial concentration [#/ul] - -s4 = P(1)*P(5) ;% T4 generation rate [#/ul-day] -s8 = P(2)*P(7) ;% T8 generation rate [#/ul-day] -sK = P(3)*P(9) ;% K generation rate [#/ul-day] -uI = P(6)*P(5) - P(15)*P(3) ;% TI decay rate constant [/day] -uC = P(8)*P(7) + P(16)*P(4)/(P(18)+P(4)) ;% TC decay rate constant [/day] - -% solving for acute-phase ------------------------------------------------- - -% Solving ODEs (see MATLAB documentation for algorithm) -[~,Yout] = ode15s(@system,t,[P(1) 0 P(2) 0 P(3) P(4)]) ; - -if any(any(Yout<0)) % if solution contains negative values - Yout = 1 ; - return -elseif size(Yout,1)~=length(t) % if solver fails - Yout = 2 ; - return -end - -% 'system' function ------------------------------------------------------- - -function dY = system(~,Y) -dY = zeros(6,1) ;% percolating dY/dt -% T4 rate of change [#/ul-day] -dY(1) = s4 - P(5)*Y(1) - P(12)*Y(6)*Y(1) ; -% TI rate of change [#/ul-day] -dY(2) = P(12)*Y(6)*Y(1) - uI*Y(2) - P(14)*Y(4)*Y(2) - P(15)*Y(5)*Y(2) ; -% T8 rate of change [#/ul-day] -dY(3) = s8 - P(7)*Y(3) - P(13)*Y(6)*Y(3) ; -% TC rate of change [#/ul-day] -dY(4) = P(13)*Y(6)*Y(3) - uC*Y(4) + P(16)*Y(6)/(P(18)+Y(6))*Y(4) ; -% K rate of change [#/ul-day] -dY(5) = sK - P(9)*Y(5) + P(17)*Y(6)/(P(19)+Y(6))*Y(5); -% V rate of change [#/ul-day] -dY(6) = P(11)*Y(2) - P(10)*Y(6) ; -end - -% preparing outputs ------------------------------------------------------- - -if nargin == 4 - Yout(:,6) = log10(Yout(:,6)*1e3) ;% converting V [log(#/ml)] -else - Yout = [log10(Yout(:,6)*1e3) ...converting V [log(#/ml)] - Yout(:,1)+Yout(:,2) ...T4+TI [#/ul] - Yout(:,3)+Yout(:,4) ...T8+TC [#/ul] - Yout(:,5) ] ;% K [#/ul] -end - -end