I don't understand the question completely. You showed, that you have applied the zero padding by padarray (a function, that I do not have) to the variable shiftedPaddedWindow. But where is this variable used later on? Where did you inster 1e-17 instead? Which size and type do the inputs have? Could you please provide some test data?
The problem is redundant because (k-1)*(n-1) replies the same values if you e.g. interchange k and n. This can be exploited to reduce the number of expensive EXP() calls.
Another idea is to move the constant expressions out of the loop:
c = -1j*2*pi/pointsToCalculate;
Y = zeros(pointsToCalculate,pointsToCalculate);
for k = 1:pointsToCalculate
Y(k,k) = y(k) * exp(c * (k-1) * (k-1));;
for n = k + 1:pointsToCalculate
d = y(n) * exp(c * (k-1) * (n-1));
Y(k,n) = d;
Y(n,k) = d;
end
end
