PC cgDNA+min: Poly A sequence

Periodic closure cgDNA+min results for the 4 initial guesses highlighted in the following bifurcation diagram:

Solutions A and D represent the same configuration. We also observe that both solutions for initial guesses A and B are not minima (minimum eigenvalue smaller than zero). In both cases, the norm of the negative eigenvalue is very small, hence we can assume that the configuration is close enough to the actual minimizer and the algorithm stopped before reaching the minimum because of a step size becoming too small.

Solution for initial guess A:

Link Energy Smallest Eigenvalue
Initial guess A 15 565 -
Solution A 15 75 -2.33e-6





MATLAB figures and saved variables:
PolyA_3Dsol1_PCcgDNA+min.fig
PolyA_2Dsol1_PCcgDNA+min_cgDNA-coord.fig
PolyA_2Dsol1_PCcgDNA+min_Pho-coord.fig
PolyA_sol1_PCcgDNA+min.mat

Solution for initial guess B:

Link Energy Smallest Eigenvalue
Initial guess B 14 1968 -
Solution B 14 272 -1.13e-4





MATLAB figures and saved variables:
PolyA_3Dsol2_PCcgDNA+min.fig
PolyA_2Dsol2_PCcgDNA+min_cgDNA-coord.fig
PolyA_2Dsol2_PCcgDNA+min_Pho-coord.fig
PolyA_sol2_PCcgDNA+min.mat

Solution for initial guess C:

Link Energy Smallest Eigenvalue
Initial guess C 16 1399 -
Solution C 16 118 6.00e-6





MATLAB figures and saved variables:
PolyA_3Dsol3_PCcgDNA+min.fig
PolyA_2Dsol3_PCcgDNA+min_cgDNA-coord.fig
PolyA_2Dsol3_PCcgDNA+min_Pho-coord.fig
PolyA_sol3_PCcgDNA+min.mat

Solution for initial guess D:

Link Energy Smallest Eigenvalue
Initial guess D 17 4234 -
Solution D 15 74 2.05e-6





MATLAB figures and saved variables:
PolyA_3Dsol4_PCcgDNA+min.fig
PolyA_2Dsol4_PCcgDNA+min_cgDNA-coord.fig
PolyA_2Dsol4_PCcgDNA+min_Pho-coord.fig
PolyA_sol4_PCcgDNA+min.mat