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NottinghamPhageN3IGPIVIIODE.m
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NottinghamPhageN3IGPIVIIODE.m
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function dy = NottinghamPhageN3IGPIVIIODE(t, y, sP)
% ODEs for a prey and two predators system
%
% Equations represent a batch system with an abiotic resource, prey species
% demonstrating monod kinetics, some of which show resistance vs predation,
% others which develop persitence to predation and two predators one
% exhibiting a Holling type I functional response, the other a type II
% and each with a seperate bdelloplast / infected cell stage.
% simMode = 15
%
% function dy = NottinghamPhageN3IGPIVIIODE(t, y, sP)
%
% dy - the rate equations
%
% t - time series
% y - initial species values
% sP - simulation parameters
% Version Author Date Affiliation
% 1.00 J K Summers 06/12/17 Kreft Lab - School of Biosciences -
% University of Birmingham
%
% Initial numbers of individuals in species being modeled
sub = y(1); % substrate value in fg/ml
senPrey = y(2); % Sensitive cells in cells / ml
bdPersistPrey = y(3); % Bdellovibrio persistor cells in cells / ml
phageResPrey = y(4); % phage resistant cells in cells / ml
bd = y(5); % Bdellovibrio cells in cells / ml
bdplast = y(6); % Bdelloplasts in cells / ml
phage = y(7); % Phage virions in virions / ml
infCell = y(8); % Infected cells in cells / ml
% Rates for processes
dSub = -(senPrey + bdPersistPrey + phageResPrey) * sP.muMaxPrey * sub / ...
((sP.Ksn + sub) * sP.yieldNPerS) + ...
sP.yieldSPerV * sP.kV * infCell + ...
sP.yieldSPerP * sP.kP * bdplast;
% Bdellovibrio persistence is phenotypic so persistor bacteria divide to
% give sensitive bacteria
dSenPrey = (senPrey + bdPersistPrey) * sP.muMaxPrey * sub / ...
(sP.Ksn + sub) - ...
bd * sP.muMaxPred1 * senPrey / sP.yieldBPerN - ...
phage * sP.muMaxPred2 * senPrey / ...
((senPrey + bdPersistPrey + phageResPrey + sP.Knv) * sP.yieldIPerN) - ...
senPrey * sP.rateDevPersist;
dBdPersistPrey = - phage * sP.muMaxPred2 * bdPersistPrey ...
/ ((senPrey + bdPersistPrey + phageResPrey + sP.Knv) * sP.yieldIPerN) + ...
senPrey * sP.rateDevPersist;
dPhageResPrey = phageResPrey * sP.muMaxPrey * sub / (sP.Ksn + sub) - ...
bd * sP.muMaxPred1 * phageResPrey / sP.yieldBPerN;
dPred1 = sP.kP * bdplast - ...
bd * sP.muMaxPred1 * (senPrey + phageResPrey) / sP.yieldBPerP - ...
sP.mortality * bd;
dBdelloplast1 = bd * sP.muMaxPred1 * (senPrey + phageResPrey) - ...
sP.kP * bdplast / sP.yieldPPerB;
dPred2 = sP.kV * infCell - ...
phage * sP.muMaxPred2 * (senPrey + bdPersistPrey) / ...
((senPrey + bdPersistPrey + phageResPrey + sP.Knv) * sP.yieldIPerV);
dBdelloplast2 = phage * sP.muMaxPred2 * (senPrey + bdPersistPrey) / ...
(senPrey + bdPersistPrey + phageResPrey + sP.Knv) - ...
sP.kV * infCell / sP.yieldVPerI;
%write results
dy = [dSub; dSenPrey; dBdPersistPrey; dPhageResPrey; dPred1; ...
dBdelloplast1; dPred2; dBdelloplast2];
end