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One_DNAs.m
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One_DNAs.m
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Fhead = [26 19.5 25.4 23.9 22 31 8 39 39 13.5 35 35 45 37 30 40 23 32 29.5 15 20 23 31 20 25 30 36 30 26 25 28.6 29.1 31 17.5 26.3 17.9 26.8 18.5 20.8 25 22.3 16.2 13.8 15.5 29 25 20 20 35 30 21.2 24 15.47 21.78 17.5 15.8 28 35 25 30 22 23 9.2 28 30.8 30 19 12 12.4 33 12.6 6 24.8 24.3 20.2 22.6 19.5 32.2 28.1 33.3 33.23 19.88 14.7 19.9 24.2 14.7 26.66 11.4 15.3];
Fhinge = [15 26 20 22.8 14.6 10.6 17.2 6.7 15 15.6 17.5 20.8 19.8 20.3 23.72 28.46 24.98 18.39 17.11 24.24 13.4];
v = 0.16; % loading rate (microns/second)
L0 = 16.32; % DNA contour length (microns), persistence length is assumed 50 nm
delta = 1.6; % force parameter (nm)
Ntrials = 2000;
T = zeros(Ntrials,1);
Fd = zeros(Ntrials,1);
N = 10000;
dt = 0.05; % time step (seconds)
k0 = 2.1e-3; % detachemnt rate (inverse seconds)
F = zeros(N,1);
L = zeros(N,1);
ypos = zeros(N,1);
ee = (rand(Ntrials,1)*1.6+8); % this is from experimental distribution measured by Martina
for j=1:Ntrials
r = rand(N,1);
x = 0;
ddx = zeros(N,1); % displacement with respect to the center of DNA
de = delta*ones(N,1);
for i=1:N
x = x + dt*v; % new position
ypos(i) = x;
L(i) = sqrt((ee(j)/2+ddx(i))^2+x*x) + sqrt((ee(j)/2-ddx(i))^2+x*x);
if L(i)>=0.9999999999999*L0
L(i) = 0.9999999999999*L0;
end
F(i) = 0.0828*(0.25/(1-L(i)/L0)/(1-L(i)/L0)-0.25+L(i)/L0); % new force in pN
alpha = atan(2*x/ee(j));
F(i) = 2*F(i)*sin(alpha);
k = k0*exp(F(i)*delta/4.14);
p = -log(1-r(i))/k;
if p<= dt
break
end
end
T(j) = i*dt;
if i<N
Fd(j) = F(i);
else
Fd(j) = 9e99;
end
end
e = 1:2:85;
n = histc(Fd,e);
n = n/max(n);
nhead = histc(Fhead,e);
nhead = nhead/max(nhead);
nhinge = histc(Fhinge,e);
nhinge = nhinge/max(nhinge);
figure
hold on
plot(e,n)
plot(e,nhead)
plot(e,nhinge)
% plot(e,nc)
legend('simulated','head','hinge')