%%%% SCRIPT NAME: DefineSpecified_2cellSyn %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%%List all cells for each receptor
%%%This code generates:
%%Syn_2cell : List of names of 2-cell synapses
%%Combo_2cell : corresponding list of cell pairs that contribute to
%%each 2-cell synapse
%%Combo_2cellR : List of receptor pairs generating each 2-cell synapse
%%Syn_3cell:  List of names of 3-cell synapses
%%Combo_3cell: List of : Original 2-cell synapse contributing to 3-cell
%%synapse;    3rd cell being added to synapse;   cell/synapse left
%%after MM-cells in 3-cell synapse are killed (or 0 if no cells are
%%killed)


ct2 = 1;

%2-synapse combos of CD3-CD28
for i3 = 1:length(Cells_CD3)
    for i28 = 1:length(Cells_CD28)
        %%Ennumerate cells and receptors in combination
        Combo_2cell(ct2,:) = {Cells_CD3{i3} Cells_CD28{i28}};
        Combo_2cellR(ct2,:) = {'CD3' 'CD28'};
        %%MODIFICATION: All cells remain in same state when join synapses, then are activated by rate below
        Syn_2cell(ct2) = {['S_' Cells_CD3{i3} '_CD3_' Cells_CD28{i28} '_CD28']};
        
        %%Specify rate of killing & Activation & transition to resistant
        %%phenotype
        %%Killing only performed by active cells - don't duplicate killing
        %%by including EM cells even though they become active in synapse
        if (strcmp(Cells_CD3{i3},'CD4_A'))
            
            if(strcmp(Cells_CD28{i28},'MM'))
                %%Active cells paired with MM can kill - set kill rate
                KillRt_2cell(ct2) = {'ps.kkillMM_CD4'};
                %%Any synapses where MM killing is possible can also
                %%transition to resistant phenotype
                Resist_2cell(ct2) = {[Syn_2cell{ct2} '_MUT']};
                ResistCells(ct2,:) = {Cells_CD3{i3} Cells_CD28{i28}};
                ResistRs(ct2,:) = {'CD3' 'CD28'};
                %No dissociation for T-cell-MM cell synapses
                DisRt_2cell(ct2) = {0};
            elseif(strcmp(Cells_CD28{i28},'TRGT'))
                %%Active cells paired with MM can kill - set kill rate
                KillRt_2cell(ct2) = {'ps.kkillTRGT_CD4'};
                %%No resistant phenotype for PBMC target cells
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                %PBMCs can dissociate over time
                DisRt_2cell(ct2) = {'ps.kDis'};
            elseif(strcmp(Cells_CD28{i28},'CD8_A')||strcmp(Cells_CD28{i28},'CD4_A'))
                %%No T-cell - T- cell killing
                KillRt_2cell(ct2) = {0};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                DisRt_2cell(ct2) = {'ps.kDis'};
            else
                KillRt_2cell(ct2) = {0};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                DisRt_2cell(ct2) = {'ps.kDis'};
            end
        elseif (strcmp(Cells_CD3{i3},'CD8_A'))
            if(strcmp(Cells_CD28{i28},'MM'))
                %% Active cells paired with MM can kill - set kill rate
                KillRt_2cell(ct2) = {'ps.kkillMM_CD8'};
                Resist_2cell(ct2) = {[Syn_2cell{ct2} '_MUT']};
                ResistCells(ct2,:) = {Cells_CD3{i3} Cells_CD28{i28}};
                ResistRs(ct2,:) = {'CD3' 'CD28'};
                DisRt_2cell(ct2) = {0};
            elseif(strcmp(Cells_CD28{i28},'TRGT'))
                %%Kill rate for PBMCs
                KillRt_2cell(ct2) = {'ps.kkillTRGT_CD8'};
                %%No resistant phenotype for PBMC target cells
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                %PBMCs can dissociate over time
                DisRt_2cell(ct2) = {'ps.kDis'};
            elseif (strcmp(Cells_CD28{i28},'CD4_A'))
                %%%No T-cell T-cell killing
                KillRt_2cell(ct2) = {0};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                DisRt_2cell(ct2) = {'ps.kDis'};
            elseif (strcmp(Cells_CD28{i28},'CD8_A'))
                KillRt_2cell(ct2) = {0};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                DisRt_2cell(ct2) = {'ps.kDis'};
            else
                KillRt_2cell(ct2) = {0};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                DisRt_2cell(ct2) = {'ps.kDis'};
            end
        else
            KillRt_2cell(ct2) = {0};
            Resist_2cell(ct2) = {'0'};
            ResistCells(ct2,:) = {'0' '0'};
            ResistRs(ct2,:) = {'0' '0'};
            DisRt_2cell(ct2) = {'ps.kDis'};
        end
        %%Activation of CD3-naive cell synapses by T-cells
        %%All T-cells bound through CD3 to CD28 cell can be activated
        if(~isempty(regexp(Cells_CD3{i3},'CD(4||8)_N','match')))  %&&(strncmp(Cells_CD28{i28},'CD',2)))
            %%Need different activation rate for CD4 and CD8??
            ActRt_2cell(ct2) = {['ps.kact_N*((X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb) + X(idx.' Syn_2cell{ct2} '_Br))/(ps.EC50_CD3*(ps.E+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb)+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3)+ X(idx.' Syn_2cell{ct2} '_Br)) +(X(idx.' ...
                Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb) + X(idx.' Syn_2cell{ct2} '_Br)))*X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)/(ps.EC50_CD28*(ps.E+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28))  +X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)))']};
            Cell = regexp(Cells_CD3{i3},'(\w+\d)_\w','tokens');  %Obtain CD4 or CD8 from name
            %%Synapse created once CD3-bound cell is activated
            Post_ActSyn(ct2) = {['S_' Cell{:}{:} '_A_CD3_' Cells_CD28{i28} '_CD28']};
            %%EM cells are activated at constant rate
        elseif (~isempty(regexp(Cells_CD3{i3},'CD(4||8)_EM','match')))  %&&(strncmp(Cells_CD28{i28},'CD',2)))
            %%Need different activation rate for CD4 and CD8??
            ActRt_2cell(ct2) = {['ps.kact_EM']};
            Cell = regexp(Cells_CD3{i3},'(\w+\d)_\w','tokens');  %Obtain CD4 or CD8 from name
            %%Synapse created once CD3-bound cell is activated
            Post_ActSyn(ct2) = {['S_' Cell{:}{:} '_A_CD3_' Cells_CD28{i28} '_CD28']};
        else
            ActRt_2cell(ct2) = {0};
            Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
        end
        
        ct2 = ct2+1;
    end
end


%%Add in 2-cell combinations with CD3 and CD38
for i3 = 1:length(Cells_CD3)
    for i38 = 1:length(Cells_CD38)
        %%Ennumerate cells and receptors in combination
        Combo_2cell(ct2,:) = {Cells_CD3{i3} Cells_CD38{i38}};
        Combo_2cellR(ct2,:) = {'CD3' 'CD38'};
        Syn_2cell(ct2) = {['S_' Cells_CD3{i3} '_CD3_' Cells_CD38{i38} '_CD38']};
        %%Specify rate of killing, activation, and synapse name - only active cells kill
        if (strncmp(Cells_CD3{i3},'CD8',3) &&(strcmp(Cells_CD38{i38},'MM')))   %%Only MM not SCD38
            %Active cells kill, no need to activate
            if (strcmp(Cells_CD3{i3},'CD8_A'))
                KillRt_2cell(ct2) = {'ps.kkillMM_CD8'};
                Resist_2cell(ct2) = {[Syn_2cell{ct2} '_MUT']};
                ResistCells(ct2,:) = {Cells_CD3{i3} Cells_CD38{i38}};
                ResistRs(ct2,:) = {'CD3' 'CD38'};
                DisRt_2cell(ct2) = {0};
                ActRt_2cell(ct2) = {0};
                Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
                %Naive cells are activated once in synapse. No killing
            elseif (strcmp(Cells_CD3{i3},'CD8_N'))
                KillRt_2cell(ct2) = {0};
                DisRt_2cell(ct2) = {'ps.kDis'};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                %%Need different activation rate for CD4 and CD8??
                ActRt_2cell(ct2) = {['ps.kact_N*((X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb) + X(idx.' Syn_2cell{ct2} '_Br))/(ps.EC50_CD3*(ps.E+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb)+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3)+ X(idx.' Syn_2cell{ct2} '_Br)) +(X(idx.' ...
                    Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb) + X(idx.' Syn_2cell{ct2} '_Br)))*X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)/(ps.EC50_CD28*(ps.E+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28)) +X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)))']};
                Post_ActSyn(ct2) = {['S_CD8_A_CD3_' Cells_CD38{i38} '_CD38']};
            elseif (strcmp(Cells_CD3{i3},'CD8_EM'))
                KillRt_2cell(ct2) = {0};
                DisRt_2cell(ct2) = {'ps.kDis'};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                %%Need different activation rate for CD4 and CD8??
                ActRt_2cell(ct2) = {['ps.kact_EM']};
                Post_ActSyn(ct2) = {['S_CD8_A_CD3_' Cells_CD38{i38} '_CD38']};
            else  %No killing or activation
                KillRt_2cell(ct2) = {0};
                DisRt_2cell(ct2) = {'ps.kDis'};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                ActRt_2cell(ct2) = {0};
                Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
            end
        elseif (strncmp(Cells_CD3{i3},'CD4',3) &&(strcmp(Cells_CD38{i38},'MM')))
            if (strcmp(Cells_CD3{i3},'CD4_A'))
                KillRt_2cell(ct2) = {'ps.kkillMM_CD4'};
                DisRt_2cell(ct2) = {0};
                Resist_2cell(ct2) = {[Syn_2cell{ct2} '_MUT']};
                ResistCells(ct2,:) = {Cells_CD3{i3} Cells_CD38{i38}};
                ResistRs(ct2,:) = {'CD3' 'CD38'};
                ActRt_2cell(ct2) = {0};
                Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
            elseif (strcmp(Cells_CD3{i3},'CD4_N'))
                KillRt_2cell(ct2) = {0};
                DisRt_2cell(ct2) = {'ps.kDis'};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                %%Need different activation rate for CD4 and CD8??
                ActRt_2cell(ct2) = {['ps.kact_N*((X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb) + X(idx.' Syn_2cell{ct2} '_Br))/(ps.EC50_CD3*(ps.E+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb)+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3)+ X(idx.' Syn_2cell{ct2} '_Br)) +(X(idx.' ...
                    Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb) + X(idx.' Syn_2cell{ct2} '_Br)))*X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)/(ps.EC50_CD28*(ps.E+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28)) +X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)))']};
                Post_ActSyn(ct2) = {['S_CD4_A_CD3_' Cells_CD38{i38} '_CD38']};
            elseif (strcmp(Cells_CD3{i3},'CD4_EM'))
                KillRt_2cell(ct2) = {0};
                DisRt_2cell(ct2) = {'ps.kDis'};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                %%Need different activation rate for CD4 and CD8??
                ActRt_2cell(ct2) = {['ps.kact_EM']};
                Post_ActSyn(ct2) = {['S_CD4_A_CD3_' Cells_CD38{i38} '_CD38']};
            else
                KillRt_2cell(ct2) = {0};
                DisRt_2cell(ct2) = {'ps.kDis'};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                ActRt_2cell(ct2) = {0};
                Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
            end
            %%%SECOND CELL IS PBMC CD38+ target cell
        elseif (strncmp(Cells_CD3{i3},'CD8',3) &&(strcmp(Cells_CD38{i38},'TRGT')))   %%Only TRGT not SCD38
            %Active cells kill, no need to activate
            if (strcmp(Cells_CD3{i3},'CD8_A'))
                KillRt_2cell(ct2) = {'ps.kkillTRGT_CD8'};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                %PBMCs can dissociate over time
                DisRt_2cell(ct2) = {'ps.kDis'};
                ActRt_2cell(ct2) = {0};
                Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
                %Naive cells are activated once in synapse. No killing
            elseif (strcmp(Cells_CD3{i3},'CD8_N'))
                KillRt_2cell(ct2) = {0};
                DisRt_2cell(ct2) = {'ps.kDis'};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                %%Need different activation rate for CD4 and CD8??
                ActRt_2cell(ct2) = {['ps.kact_N*((X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb) + X(idx.' Syn_2cell{ct2} '_Br))/(ps.EC50_CD3*(ps.E+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb)+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3)+ X(idx.' Syn_2cell{ct2} '_Br)) +(X(idx.' ...
                    Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb) + X(idx.' Syn_2cell{ct2} '_Br)))*X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)/(ps.EC50_CD28*(ps.E+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28)) +X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)))']};
                Post_ActSyn(ct2) = {['S_CD8_A_CD3_' Cells_CD38{i38} '_CD38']};
            elseif (strcmp(Cells_CD3{i3},'CD8_EM'))
                KillRt_2cell(ct2) = {0};
                DisRt_2cell(ct2) = {'ps.kDis'};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                %%Need different activation rate for CD4 and CD8??
                ActRt_2cell(ct2) = {['ps.kact_EM']};
                Post_ActSyn(ct2) = {['S_CD8_A_CD3_' Cells_CD38{i38} '_CD38']};
            else  %No killing or activation
                KillRt_2cell(ct2) = {0};
                DisRt_2cell(ct2) = {'ps.kDis'};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                ActRt_2cell(ct2) = {0};
                Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
            end
        elseif (strncmp(Cells_CD3{i3},'CD4',3) &&(strcmp(Cells_CD38{i38},'TRGT')))
            if (strcmp(Cells_CD3{i3},'CD4_A'))
                KillRt_2cell(ct2) = {'ps.kkillTRGT_CD4'};
                DisRt_2cell(ct2) = {'ps.kDis'};
                Resist_2cell(ct2) = {['0']};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                ActRt_2cell(ct2) = {0};
                Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
            elseif (strcmp(Cells_CD3{i3},'CD4_N'))
                KillRt_2cell(ct2) = {0};
                DisRt_2cell(ct2) = {'ps.kDis'};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                %%Need different activation rate for CD4 and CD8??
                ActRt_2cell(ct2) = {['ps.kact_N*((X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb) + X(idx.' Syn_2cell{ct2} '_Br))/(ps.EC50_CD3*(ps.E+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb)+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3) + X(idx.' Syn_2cell{ct2} '_Br)) +(X(idx.' ...
                    Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD3_tsAb) + X(idx.' Syn_2cell{ct2} '_Br)))*X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)/(ps.EC50_CD28*(ps.E+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)+X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28)) +X(idx.' Syn_2cell{ct2} '_R_' Cells_CD3{i3} '_CD28_tsAb)))']};
                Post_ActSyn(ct2) = {['S_CD4_A_CD3_' Cells_CD38{i38} '_CD38']};
            elseif (strcmp(Cells_CD3{i3},'CD4_EM'))
                KillRt_2cell(ct2) = {0};
                DisRt_2cell(ct2) = {'ps.kDis'};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                %%Need different activation rate for CD4 and CD8??
                ActRt_2cell(ct2) = {['ps.kact_EM']};
                Post_ActSyn(ct2) = {['S_CD4_A_CD3_' Cells_CD38{i38} '_CD38']};
            else
                KillRt_2cell(ct2) = {0};
                DisRt_2cell(ct2) = {'ps.kDis'};
                Resist_2cell(ct2) = {'0'};
                ResistCells(ct2,:) = {'0' '0'};
                ResistRs(ct2,:) = {'0' '0'};
                ActRt_2cell(ct2) = {0};
                Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
            end
        else
            %%Cells connected to sCD38 do not become active or kill
            KillRt_2cell(ct2) = {0};
            DisRt_2cell(ct2) = {'ps.kDis'};
            Resist_2cell(ct2) = {'0'};
            ResistCells(ct2,:) = {'0' '0'};
            ResistRs(ct2,:) = {'0' '0'};
            ActRt_2cell(ct2) = {0};
            Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
        end
        
        ct2 = ct2+1;
    end
end


%%Add in 2-cell combinations with CD28 and CD38
for i28 = 1:length(Cells_CD28)
    for i38 = 1:length(Cells_CD38)
        %%Ennumerate cells and receptors in combination
        Combo_2cell(ct2,:) = {Cells_CD28{i28} Cells_CD38{i38}};
        Combo_2cellR(ct2,:) = {'CD28' 'CD38'};
        %%EM T-cells connected to CD28 arm do not become active
        Syn_2cell(ct2) = {['S_' Cells_CD28{i28} '_CD28_' Cells_CD38{i38} '_CD38']};
        %%Specify rate of killing if first cell is T-cell - only active
        %%T-cells kill
        %%%No activation possible here - activated cells kill and emit
        %%%cytokines
        if (strcmp(Cells_CD28{i28},'CD8_A') &&(strcmp(Cells_CD38{i38},'MM')))
            KillRt_2cell(ct2) = {'ps.kkillMM_CD8'};
            DisRt_2cell(ct2) = {0};
            Resist_2cell(ct2) = {[Syn_2cell{ct2} '_MUT']};
            ResistCells(ct2,:) = {Cells_CD28{i28} Cells_CD38{i38}};
            ResistRs(ct2,:) = {'CD28' 'CD38'};
            ActRt_2cell(ct2) = {0};
            Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
        elseif (strcmp(Cells_CD28{i28},'CD4_A') &&(strcmp(Cells_CD38{i38},'MM')))
            KillRt_2cell(ct2) = {'ps.kkillMM_CD4'};
            DisRt_2cell(ct2) = {0};
            Resist_2cell(ct2) = {[Syn_2cell{ct2} '_MUT']};
            ResistCells(ct2,:) = {Cells_CD28{i28} Cells_CD38{i38}};
            ResistRs(ct2,:) = {'CD28' 'CD38'};
            ActRt_2cell(ct2) = {0};
            Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
        elseif (strcmp(Cells_CD28{i28},'CD8_A') &&(strcmp(Cells_CD38{i38},'TRGT')))   %%Only TRGT not SCD38
            KillRt_2cell(ct2) = {'ps.kkillTRGT_CD8'};
            DisRt_2cell(ct2) = {'ps.kDis'};
            %No resistant phenotypes for target cells
            Resist_2cell(ct2) = {'0'};
            ResistCells(ct2,:) = {'0' '0'};
            ResistRs(ct2,:) = {'0' '0'};
            ActRt_2cell(ct2) = {0};
            Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
        elseif (strcmp(Cells_CD28{i28},'CD4_A') &&(strcmp(Cells_CD38{i38},'TRGT')))
            KillRt_2cell(ct2) = {'ps.kkillTRGT_CD4'};
            DisRt_2cell(ct2) = {'ps.kDis'};
            Resist_2cell(ct2) = {'0'};
            ResistCells(ct2,:) = {'0' '0'};
            ResistRs(ct2,:) = {'0' '0'};
            ActRt_2cell(ct2) = {0};
            Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
        else
            KillRt_2cell(ct2) = {0};
            DisRt_2cell(ct2) = {'ps.kDis'};
            Resist_2cell(ct2) = {'0'};
            ResistCells(ct2,:) = {'0' '0'};
            ResistRs(ct2,:) = {'0' '0'};
            ActRt_2cell(ct2) = {0};
            Post_ActSyn(ct2) = Syn_2cell(ct2);  %No change
        end
        
        ct2 = ct2+1;
    end
end

%%cytokine production sums for each synapsed cell
for cyt = 1:ct2-1
    
    %%%T-cells must be involved in synapse for cytokine production
    if((strcmp(Combo_2cell{cyt,1},'TRGT')&& strcmp(Combo_2cell{cyt,2},'TRGT')) || (strcmp(Combo_2cell{cyt,1},'MM')&& strcmp(Combo_2cell{cyt,2},'MM'))...
            || (strcmp(Combo_2cell{cyt,1},'MM')&& strcmp(Combo_2cell{cyt,2},'TRGT')))
        SynprIFNg(cyt) = {0} ;
        SynprTNFa(cyt) = {0} ;
        SynprIL6(cyt) = {0} ;
        SynprIL10(cyt) = {0} ;
    else
        SynprIFNg(cyt) = {['(ps.kprod_' Combo_2cell{cyt,1} '_IFNg + ps.kprod_' Combo_2cell{cyt,2} '_IFNg)']} ;
        SynprTNFa(cyt) ={['(ps.kprod_' Combo_2cell{cyt,1} '_TNFa + ps.kprod_' Combo_2cell{cyt,2} '_TNFa)']} ;
        SynprIL6(cyt) = {['(ps.kprod_' Combo_2cell{cyt,1} '_IL6 + ps.kprod_' Combo_2cell{cyt,2} '_IL6)']} ;
        SynprIL10(cyt) = {['(ps.kprod_' Combo_2cell{cyt,1} '_IL10 + ps.kprod_' Combo_2cell{cyt,2} '_IL10)']} ;
    end
end

%%Above lists will be used for kon/koff terms. For kkill, need unique
%%list - last accesses active cell synapses in duplicate listings of EM and
%%active cells both contributing to active synapse
[Syn2Cell_Unq,udex2] = unique(Syn_2cell,'last');
SynKill_2Cell = KillRt_2cell(udex2);
Cells_Syn2_Unq = Combo_2cell(udex2,:);
Rs_Syn2_Unq = Combo_2cellR(udex2,:);
Act_2cell_Unq = ActRt_2cell(udex2);
PostAct_Unq = Post_ActSyn(udex2);  %No change
Resist_SynUnq = Resist_2cell(udex2);
ResistCells_SynUnq = ResistCells(udex2,:);
ResistRs_SynUnq = ResistRs(udex2,:) ;
DisRt_2cell_Unq = DisRt_2cell(udex2);
IFNg_Unq = SynprIFNg(udex2);
TNFa_Unq = SynprTNFa(udex2);
IL6_Unq = SynprIL6(udex2);
IL10_Unq = SynprIL10(udex2);

%Create list of total unique synapses including resistant synapses
[Resist_Unq,rdex2] = unique(Resist_SynUnq,'last');
%%Remove 0 if present
if ((Resist_Unq{1}=='0'))
    Resist_Unq = Resist_Unq(2:end);
    rdex2= rdex2(2:end);
end

ResistCells_Unq = ResistCells_SynUnq(rdex2,:);
ResistRs_Unq = ResistRs_SynUnq(rdex2,:) ;
Syn2Cell_UnqTOT =   [Syn2Cell_Unq Resist_Unq];
Cells_Syn2_UnqTOT =   [Cells_Syn2_Unq; ResistCells_Unq];
Rs_Syn2_UnqTOT = [Rs_Syn2_Unq; ResistRs_Unq];
%%Dissociation should be added for resistant cell synapses
for i = 1:length(Resist_Unq)
    Dist_R(i) = {'ps.kDis'};
end
DisRt_2cell_UnqTOT = [DisRt_2cell_Unq Dist_R];