Analysis-code/ZMW_sim_Gelsolin_4Steps.m at master · BioMolecularSelfOrganizationLab/Analysis-code · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
function [simZMW] = ZMW_sim_Gelsolin_4Steps(Ac,cycles)

% Ac = 0.8;
rates_onR = [0.1 0.3 0.6];
rates_on = rates_onR.*Ac;
rates_off = [0 0.2 3];


% cycles = 9;
SNR =0;

h = waitbar(0,'Please wait, simulating traces...');

for i = 1:cycles
    clear MonTre t tM  k tMon Mon
    waitbar(i / cycles)

    %     clear all
    Ttot = 800;
    dt = 0.2;
    ttot = Ttot/dt;
    Mon = zeros(ttot,1);
    MonTre = zeros(ttot,1);
    tM = zeros(ttot,1);

    k = 1;
    t = [dt:dt:Ttot];
    tM0 = random(makedist('exp',1/rates_on(1)));
    tMon(1) = round(tM0./dt);
    Mon(tMon(1)+1) = 1;
    tM(1) = tM0;

    while sum(tMon) < ttot
%         sum(tM);
%         tic
        k = k+1;
        MonTre = cumsum(Mon);


        tM3 = random(makedist('exp',1/rates_on(3)));
        tM4 = random(makedist('exp',1/rates_off(3)));
        kon3 = round(tM3./dt);
        koff3 = round(tM4./dt);


        if MonTre(end) == 1

            tM1 = random(makedist('exp',1/rates_on(2)));
            kon2 = round(tM1./dt);
            tMon(k) = kon2;
            tM(k) = tM1;
            Mon(sum(tMon(1:k))+1) = 1;

        elseif MonTre(end) == 2
            tM2 = random(makedist('exp',1/rates_off(2)));
            koff2 = round(tM2./dt);
            tM3 = random(makedist('exp',1/rates_on(3)));
            kon3 = round(tM3./dt);

            if kon3 < koff2
                tMon(k) = kon3;
                tM(k) = tM3;
                Mon(sum(tMon(1:k))+1) = 1;

            else
                tMon(k) = koff2;
                tM(k) = tM2;
                Mon(sum(tMon(1:k))+1) = -1;
            end


        else
            tM3 = random(makedist('exp',1/rates_on(3)));
            tM4 = random(makedist('exp',1/rates_off(3)));
            kon3 = round(tM3./dt);
            koff3 = round(tM4./dt);


            if kon3 < koff3
                tMon(k) = kon3;
                tM(k) = tM3;
                Mon(sum(tMon(1:k))+1) = 1;

            else
                tMon(k) = koff3;
                tM(k) = tM4;
                Mon(sum(tMon(1:k))+1) = -1;
            end

        end

        %         koff3 < kon3 & MonTre(end) > 2 & MonTre(end) > 0
        %         tMon(k) = koff3;
        %         tM(k) = tM4;
        %         Mon(sum(tMon(1:k))+1) = -1;
        %
        %         kon2 < koff2 & MonTre(end) == 1
        %         tMon(k) = kon2;
        %         tM(k) = tM1;
        %         Mon(sum(tMon(1:k))+1) = 1;


    end
%     toc
    simZMW.time{i} = t;
    simZMW.monomers{i} = MonTre;
    simZMW.Tmon{i} = tMon;
    simZMW.TM{i} = tM;
    simZMW.noise{i} = MonTre + (1/SNR)*randn(numel(MonTre),1);
    %     toc

end
simZMW.cycles = cycles;

close(h)

if cycles == 1
    tdum1 = cell2mat(simZMW.noise);
    tdum2 = cell2mat(simZMW.monomers);
    figure
    plot(t,tdum1,'Color',[0.8 0.8 0.8])
    hold on
    plot(t,tdum2,'k')
    xlabel( ' Time (s)' );
    ylabel( 'Intensity (a.u.)' );
elseif cycles == 9
    figure
    tdum1 = cell2mat(simZMW.noise);
    tdum2 = cell2mat(simZMW.monomers);
    for j = 1:cycles
        subplot(3,3,j)
        plot(t,tdum1(:,j),'Color',[0.8 0.8 0.8])
        hold on
        plot(t,tdum2(:,j),'k')
        xlabel( ' Time (s)' );
        ylabel( 'Intensity (a.u.)' );
    end
end