Tutorial on retaining residual strain and cutting
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Note
Crimson: code relating to submodel selection
MediumBlue: code to tell plotter to put morphogens on their respective A and B sides
RosyBrown: code for setting up the seam and cutting the mesh
When the system is arrested (ARRESTTIME=50) there is no further growth and the seams are cut. (The dummy morphogen f_seams is used to specify the nodes that will be divided into two, unconnected nodes - by declaring the morphogen in the GUI it is easy to check that the cuts will be in the right place. There is a plot option to allow the seams to be seen.)
% Section 1 function m = gpt_retainstrainandcut_20110603( m ) %m = gpt_retainstrainandcut_20110603( m ) % Morphogen interaction function. % Written at 2011-06-03 14:38:33. % GFtbox revision 3554, 2011-06-02 12:30:52.789869. % The user may edit any part of this function between delimiters % of the form "USER CODE..." and "END OF USER CODE...". The % delimiters themselves must not be moved, edited, deleted, or added. if isempty(m), return; end fprintf( 1, '%s found in %s\n', mfilename(), which(mfilename()) ); try m = local_setproperties( m ); catch end realtime = m.globalDynamicProps.currenttime; % Section 2 %%% USER CODE: INITIALISATION % In this section you may modify the mesh in any way whatsoever. if Steps(m)==0 % First iteration m.userdata.ranges.modelname.range = { 'NORESIDUALS', 'FULLRESIDUALS' }; m.userdata.ranges.modelname.index = 1; end modelname = m.userdata.ranges.modelname.range{m.userdata.ranges.modelname.index}; switch modelname case 'NORESIDUALS' % Set up the parameters (e.g. mutations) for this model here. StrainRetention=0; case 'FULLRESIDUALS' % Set up the parameters (e.g. mutations) for this model here. StrainRetention=1; otherwise % If you reach here, you probably forgot a case. end % override the GUI and plot the two growth rates on the different sides % this line must be commented out if you want to watch the residual % strain build up and decay (Plot output value, Residual growth, Areal) m = leaf_plotoptions( m, 'morphogenA', 'KAPAR','morphogenB', 'KBPAR'); % There is a bug in the code that colours in the mesh and colourbar % The work around is to click the Monochrome tick box off and on again % likewise the Auto color range % For this example it is best to turn off the auto color range %%% END OF USER CODE: INITIALISATION % Section 3 %%% SECTION 1: ACCESSING MORPHOGENS AND TIME. %%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT. if isempty(m), return; end setGlobals(); global gNEW_KA_PAR gNEW_KA_PER gNEW_KB_PAR gNEW_KB_PER global gNEW_K_NOR gNEW_POLARISER gNEW_STRAINRET gNEW_ARREST dt = m.globalProps.timestep; polariser_i = gNEW_POLARISER; P = m.morphogens(:,polariser_i); [kapar_i,kapar_p,kapar_a,kapar_l] = getMgenLevels( m, 'KAPAR' ); [kaper_i,kaper_p,kaper_a,kaper_l] = getMgenLevels( m, 'KAPER' ); [kbpar_i,kbpar_p,kbpar_a,kbpar_l] = getMgenLevels( m, 'KBPAR' ); [kbper_i,kbper_p,kbper_a,kbper_l] = getMgenLevels( m, 'KBPER' ); [knor_i,knor_p,knor_a,knor_l] = getMgenLevels( m, 'KNOR' ); [strainret_i,strainret_p,strainret_a,strainret_l] = getMgenLevels( m, 'STRAINRET' ); [arrest_i,arrest_p,arrest_a,arrest_l] = getMgenLevels( m, 'ARREST' ); [id_sidelines_i,id_sidelines_p,id_sidelines_a,id_sidelines_l] = getMgenLevels( m, 'ID_SIDELINES' ); [id_topcap_i,id_topcap_p,id_topcap_a,id_topcap_l] = getMgenLevels( m, 'ID_TOPCAP' ); [id_botcap_i,id_botcap_p,id_botcap_a,id_botcap_l] = getMgenLevels( m, 'ID_BOTCAP' ); [f_seam_i,f_seam_p,f_seam_a,f_seam_l] = getMgenLevels( m, 'F_SEAM' ); % Mesh type: capsule % basecap: 1 % baseheight: 1 % baserings: 5 % circumdivs: 12 % height: 0.2 % heightdivs: 16 % randomness: 0.1 % topcap: 1 % topheight: 1 % toprings: 5 % version: 1 % xwidth: 0.2 % ywidth: 0.2 % Morphogen Diffusion Decay Dilution Mutant % ------------------------------------------------- % KAPAR ---- ---- ---- ---- % KAPER ---- ---- ---- ---- % KBPAR ---- ---- ---- ---- % KBPER ---- ---- ---- ---- % KNOR ---- ---- ---- ---- % POLARISER 0.002 ---- ---- ---- % STRAINRET ---- ---- ---- ---- % ARREST ---- ---- ---- ---- % ID_SIDELINES ---- ---- ---- ---- % ID_TOPCAP ---- ---- ---- ---- % ID_BOTCAP ---- ---- ---- ---- % F_SEAM ---- ---- ---- ---- %%% USER CODE: MORPHOGEN INTERACTIONS % In this section you may modify the mesh in any way that does not % Section 4 % alter the set of nodes. if Steps(m)==0 % Initialisation code. % Put any code here that should only be performed at the start of % the simulation, for example, to set up initial morphogen values. % Force global variables to zeros to make debugging more reliable m.morphogens=zeros(size(m.morphogens)); m.seams=logical(zeros(size(m.seams))); m.polfreeze=zeros(size(m.polfreeze)); m.mgen_production=zeros(size(m.mgen_production)); % Caps id_topcap_p(m.nodes(:,3)>0.17)=1; id_botcap_p(m.nodes(:,3)<-0.17)=1; % Sidelines indx=find(abs(m.nodes(:,1))>0.08); indy=find(abs(m.nodes(:,2))<0.02); id_sidelines_p(intersect(indx,indy))=1; % Seams along which the capsule will be cut (not the bottom cap) inds=[find(id_sidelines_p>0.5);find(id_topcap_p>0.5)]; f_seam_p(inds)=1; m=leaf_set_seams(m,f_seam_p); % Seams will be cut when this flag is set to 1 - see see FINALISATION code m.userdata.CutOpen=0; end % Section 5 % Code common to all models. (the different strain retention is setup % in the initial routines above) strainret_p=StrainRetention.*ones(size(strainret_p)); ARRESTTIME=50; if m.userdata.CutOpen==0 % Grow the silique % Section 6 % Code for specific models. % @@PRN Polariser Regulatory Network % Every equation to be formatted should end with an at-at Eqn N comment. m = leaf_mgen_conductivity( m, 'Polariser', 0.002);% diffusion constant m = leaf_mgen_dilution( m, 'Polariser', false );% it will not dilute with growth m = leaf_mgen_absorption( m, 'Polariser', 0); % it will not decay everywhere P(id_topcap_l>0.5)=1; m.morphogenclamp(id_topcap_l>0.5,polariser_i) = 1; P(id_botcap_l>0.5)=0; m.morphogenclamp(id_botcap_l>0.5,polariser_i) = 1; % having clamped the values at each end and allowed POL to diffuse % diffusion will occur automatically and produce a linear gradient kapar_p=0.01; % Specified growth on the inside kbpar_p=0.001; % Much less specified growth on the outside kaper_p=0.2*kapar_p; % anisotropic growth (grows lengthwise) kbper_p=0.2*kbpar_p; if realtime>ARRESTTIME m.userdata.CutOpen=1; end elseif m.userdata.CutOpen==1 else % relax the cut silique kapar_p=0; kbpar_p=0; kaper_p=0; kbper_p=0; knor_p =0; m = leaf_setproperty( m, 'freezing', 0.9 ); end % Section 7 %%% END OF USER CODE: MORPHOGEN INTERACTIONS %%% SECTION 3: INSTALLING MODIFIED VALUES BACK INTO MESH STRUCTURE %%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT. m.morphogens(:,polariser_i) = P; m.morphogens(:,kapar_i) = kapar_p; m.morphogens(:,kaper_i) = kaper_p; m.morphogens(:,kbpar_i) = kbpar_p; m.morphogens(:,kbper_i) = kbper_p; m.morphogens(:,knor_i) = knor_p; m.morphogens(:,strainret_i) = strainret_p; m.morphogens(:,arrest_i) = arrest_p; m.morphogens(:,id_sidelines_i) = id_sidelines_p; m.morphogens(:,id_topcap_i) = id_topcap_p; m.morphogens(:,id_botcap_i) = id_botcap_p; m.morphogens(:,f_seam_i) = f_seam_p; %%% USER CODE: FINALISATION % In this section you may modify the mesh in any way whatsoever. if m.userdata.CutOpen==1 m=leaf_dissect(m); m.userdata.CutOpen=2; m = leaf_setproperty( m, 'freezing', 0.999 ); end %%% END OF USER CODE: FINALISATION end %%% USER CODE: SUBFUNCTIONS % Here you may add any functions of your own, that you want to call from % the interaction function, but never need to call from outside it. % Whichever section they are called from, they must respect the same % restrictions on what modifications they are allowed to make to the mesh. % This comment can be deleted.