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ts_simStep.m
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%% Step simulations
function ts_simStep(bs,beta,gamma,delta,psi,mu,taut,edpc,rpc,ststn)
%% Specify parameters for initical configurations
% Here, we categorize these parameterse into two categories, geometric
% parameters and mechanical parameters. Denote a set of geometric
% parameters as 'gm_p' and a set of mechanical parameters as 'mc_p'. If
% we want to add paramters, just add more elements in each variable.
[gmp,mcp]=deal(struct);
[gmp.tgAr,gmp.sstn,gmp.bs,gmp.edpc]=deal(1,0,bs,edpc);
[mcp.beta,mcp.gam,mcp.del,mcp.psi,mcp.mu,mcp.taut]=...
deal(beta,gamma,delta,psi,mu,taut);
[gmp.nFa,gmp.lsc,gmp.dt]=...
deal(gmp.bs^2,mcp.psi*sqrt(gmp.tgAr),0.005);
gmp.shEd=0.01*2*sqrt(pi);
%% Generate initial configuration
[vrtx,edge,face,rg]=ts_initialConf(gmp.bs);
% set an initial tension as fixed point tension
for ii=1:size(edge{1},1)
edge{1}(ii,rg.ei(3))=ts_edgeFixedTension(face,edge,rg,mcp,ii);
end
%% Introduce extracellular space cells
for ii=1:size(vrtx,1)
[vrtx,edge,face,gmp]=...
ts_t2ReverseTransition(vrtx,edge,face,rg,gmp,mcp,ii);
end
%% Relaxation of the configuration with extracellular spaces.
mcp.mu=mu;
[itc,ttMx,ttTm]=deal(0,4*mcp.taut+8*gmp.dt,0);
gmp.shEd=0.01*2*sqrt(pi);
while (ttTm<=ttMx)
gmp.eLnc=ts_edgeLenAll(edge,gmp);
[vrtx,edge,face]=ts_iteration(vrtx,edge,face,rg,gmp,mcp);
itc=itc+1;
ttTm=ttTm+gmp.dt;
if mod(itc,3)==0
[vrtx,edge,face,gmp]=...
ts_topTransitionType1(vrtx,edge,face,rg,gmp,mcp);
end
if mod(itc,5)==1
[vrtx,edge,face,gmp]=...
ts_topTransitionType3(vrtx,edge,face,rg,gmp,mcp);
end
if mod(itc,5)==2
%% Compute t4t1 transition
for ii=1:size(vrtx,1)
[vrtx,edge,face]=...
ts_t4AdjacentTransition(vrtx,edge,face,rg,gmp,mcp,ii);
end
end
if mod(itc,5)==3
[vrtx,edge,face,gmp]=...
ts_topTransitionType2(vrtx,edge,face,rg,gmp,mcp);
end
end
%% Relaxation of the configuration with extracellular spaces.
[itc,ttMx,ttTm,exc]=deal(0,60*mcp.taut,0,1);
ttDtPt=ttMx/gmp.dt/10;
dtPt=4000;
dtc=1;
[vr,ed1,ed2,ed3,ed4,fa1,fa2,fa3]=deal(cell(min(dtPt,ttDtPt),1));
stnAll=zeros(min(dtPt,ttDtPt),1);
odir=sprintf('step/psi%s_gam%s_mu%s/',num2str(psi),...
num2str(gamma),num2str(mu));
odir=strrep(odir,'.','d');
if ~exist(odir,'dir')
mkdir(odir);
end
while (ttTm<=2*mcp.taut)
gmp.eLnc=ts_edgeLenAll(edge,gmp);
[vrtx,edge,face]=ts_iteration(vrtx,edge,face,rg,gmp,mcp);
itc=itc+1;
ttTm=ttTm+gmp.dt;
if mod(itc,3)==0
[vrtx,edge,face,gmp]=...
ts_topTransitionType1(vrtx,edge,face,rg,gmp,mcp);
end
if mod(itc,5)==1
[vrtx,edge,face,gmp]=...
ts_topTransitionType3(vrtx,edge,face,rg,gmp,mcp);
end
if mod(itc,5)==2
%% Compute t4t1 transition
for ii=1:size(vrtx,1)
[vrtx,edge,face]=...
ts_t4AdjacentTransition(vrtx,edge,face,rg,gmp,mcp,ii);
end
end
if mod(itc,5)==3
[vrtx,edge,face,gmp]=...
ts_topTransitionType2(vrtx,edge,face,rg,gmp,mcp);
end
if mod(itc,10)==3
[vr{exc},ed1{exc},ed2{exc},ed3{exc},ed4{exc},fa1{exc},...
fa2{exc},fa3{exc}]=deal(vrtx,edge{1},edge{2},edge{3},...
edge{4},face{1},face{2},face{3});
stnAll(exc)=gmp.sstn;
exc=exc+1;
if exc==dtPt+1
save(sprintf('%s/vr_r%d_d%d.mat',odir,rpc,dtc),'vr');
save(sprintf('%s/ed1_r%d_d%d.mat',odir,rpc,dtc),'ed1');
save(sprintf('%s/ed2_r%d_d%d.mat',odir,rpc,dtc),'ed2');
save(sprintf('%s/ed3_r%d_d%d.mat',odir,rpc,dtc),'ed3');
save(sprintf('%s/ed4_r%d_d%d.mat',odir,rpc,dtc),'ed4');
save(sprintf('%s/fa1_r%d_d%d.mat',odir,rpc,dtc),'fa1');
save(sprintf('%s/fa2_r%d_d%d.mat',odir,rpc,dtc),'fa2');
save(sprintf('%s/fa3_r%d_d%d.mat',odir,rpc,dtc),'fa3');
save(sprintf('%s/stn_r%d_d%d.mat',odir,rpc,dtc),'stnAll');
dtc=dtc+1;
exc=1;
ttDtPt=ttDtPt-dtPt;
[vr,ed1,ed2,ed3,ed4,fa1,fa2,fa3]=...
deal(cell(min(dtPt,ttDtPt),1));
stnAll=zeros(min(dtPt,ttDtPt),1);
end
end
end
%% Apply step strain
gmp.sstn=ststn;
vrtx(:,rg.vi(3))=vrtx(:,rg.vi(3))+ststn*vrtx(:,rg.vi(3)+1);
for edc=1:size(edge{2},1)
emd=edge{2}{edc};
emd(:,1)=emd(:,1)+ststn*emd(:,2);
edge{2}{edc}=emd;
end
%% Relax configurations.
while (ttTm<=ttMx)
gmp.eLnc=ts_edgeLenAll(edge,gmp);
[vrtx,edge,face]=ts_iteration(vrtx,edge,face,rg,gmp,mcp);
itc=itc+1;
ttTm=ttTm+gmp.dt;
if mod(itc,3)==0
[vrtx,edge,face,gmp]=...
ts_topTransitionType1(vrtx,edge,face,rg,gmp,mcp);
end
if mod(itc,5)==1
[vrtx,edge,face,gmp]=...
ts_topTransitionType1(vrtx,edge,face,rg,gmp,mcp);
end
if mod(itc,5)==2
%% Compute t4t1 transition
for ii=1:size(vrtx,1)
[vrtx,edge,face]=...
ts_t4AdjacentTransition(vrtx,edge,face,rg,gmp,mcp,ii);
end
end
if mod(itc,5)==3
[vrtx,edge,face,gmp]=...
ts_topTransitionType1(vrtx,edge,face,rg,gmp,mcp);
end
if mod(itc,10)==3
[vr{exc},ed1{exc},ed2{exc},ed3{exc},ed4{exc},fa1{exc},...
fa2{exc},fa3{exc}]=deal(vrtx,edge{1},edge{2},edge{3},...
edge{4},face{1},face{2},face{3});
stnAll(exc)=gmp.sstn;
exc=exc+1;
if exc==dtPt+1
save(sprintf('%s/vr_r%d_d%d.mat',odir,rpc,dtc),'vr');
save(sprintf('%s/ed1_r%d_d%d.mat',odir,rpc,dtc),'ed1');
save(sprintf('%s/ed2_r%d_d%d.mat',odir,rpc,dtc),'ed2');
save(sprintf('%s/ed3_r%d_d%d.mat',odir,rpc,dtc),'ed3');
save(sprintf('%s/ed4_r%d_d%d.mat',odir,rpc,dtc),'ed4');
save(sprintf('%s/fa1_r%d_d%d.mat',odir,rpc,dtc),'fa1');
save(sprintf('%s/fa2_r%d_d%d.mat',odir,rpc,dtc),'fa2');
save(sprintf('%s/fa3_r%d_d%d.mat',odir,rpc,dtc),'fa3');
save(sprintf('%s/stn_r%d_d%d.mat',odir,rpc,dtc),'stnAll');
dtc=dtc+1;
exc=1;
ttDtPt=ttDtPt-dtPt;
[vr,ed1,ed2,ed3,ed4,fa1,fa2,fa3]=...
deal(cell(min(dtPt,ttDtPt),1));
stnAll=zeros(min(dtPt,ttDtPt),1);
end
end
end
if exc>1
save(sprintf('%s/vr_r%d_d%d.mat',odir,rpc,dtc),'vr');
save(sprintf('%s/ed1_r%d_d%d.mat',odir,rpc,dtc),'ed1');
save(sprintf('%s/ed2_r%d_d%d.mat',odir,rpc,dtc),'ed2');
save(sprintf('%s/ed3_r%d_d%d.mat',odir,rpc,dtc),'ed3');
save(sprintf('%s/ed4_r%d_d%d.mat',odir,rpc,dtc),'ed4');
save(sprintf('%s/fa1_r%d_d%d.mat',odir,rpc,dtc),'fa1');
save(sprintf('%s/fa2_r%d_d%d.mat',odir,rpc,dtc),'fa2');
save(sprintf('%s/fa3_r%d_d%d.mat',odir,rpc,dtc),'fa3');
save(sprintf('%s/stn_r%d_d%d.mat',odir,rpc,dtc),'stnAll');
end
end