MATLAB scripts
Matlab scripts can be downloaded from the following .zip file: Federica_Computations_folder.zip.The scripts then runs the discrete energy minimization for all combinations of models and boundaries.
The initial guesses are read from the "Initial_guesses" folder.
The function that runs the minimization is the find_min_e function, for bBDNA initial guess, and find_min_e_inters function, for bBDNA with gd intras. The function to compute the energy, its gradient and Hessian is discrete_dna_penalty_en_grad_hess. The definitions of both funcitons can be found in the .m files with the corresponding names.
Before running the following codes it is necessary to set in the find_min_e and find_min_e_inters functions, in particular in fminunc function, the chosen optimization algorithm, that can be Trust Region or Quasi-Newton.
Kahn_Crothers.m
| Inputs | bBDNA initial guesses read from 'Initial_guesses' folder |
| guesses must be named: | |
| Parameters | model for DNA: models "cgDNA+min" |
| sequence: range_guesses: list of ‹guess_nb› | |
| Outputs | 3D views of bBDNA solution, name: Results/3D_views/‹seq_name›_guess‹guess_nb›_‹model›.png |
| 3D views of bBDNAgd solution, name: Results/3D_views/‹seq_name›_3Dsol‹guess_nb›_‹model›.png | |
| 2D plots of solution, name: Results/2D_plots/‹seq_name›_2Dsol‹guess_nb›_‹model›.png | |
| 2D plots of solution, name: Results/2D_plots/‹seq_name›_2Dsol‹guess_nb›_‹model›.png | |
| MATLBAL variables: Energy, Gradient, Hessian eigenvalues, Hessian condition number, Difference of the two obtained solutions |
Widom_601_94bp.m
| Inputs | bBDNA initial guesses read from 'Initial_guesses' folder |
| guesses must be named: | |
| Parameters | model for DNA: models "cgDNA+min" |
| sequence: range_guesses: list of ‹guess_nb› | |
| Outputs | 3D views of bBDNA solution, name: Results/3D_views/‹seq_name›_guess‹guess_nb›_‹model›.png |
| 3D views of bBDNAgd solution, name: Results/3D_views/‹seq_name›_3Dsol‹guess_nb›_‹model›.png | |
| 2D plots of solution, name: Results/2D_plots/‹seq_name›_2Dsol‹guess_nb›_‹model›.png | |
| 2D plots of solution, name: Results/2D_plots/‹seq_name›_2Dsol‹guess_nb›_‹model›.png | |
| MATLBAL variables: Energy, Gradient, Hessian eigenvalues, Hessian condition number, Difference of the two obtained solutions |
Noy_251bp.m
| Inputs | bBDNA initial guesses read from 'Initial_guesses' folder |
| guesses must be named: | |
| Parameters | model for DNA: models "cgDNA+min" |
| sequence: range_guesses: list of ‹guess_nb› | |
| Outputs | 3D views of bBDNA solution, name: Results/3D_views/‹seq_name›_guess‹guess_nb›_‹model›.png |
| 3D views of bBDNAgd solution, name: Results/3D_views/‹seq_name›_3Dsol‹guess_nb›_‹model›.png | |
| 2D plots of solution, name: Results/2D_plots/‹seq_name›_2Dsol‹guess_nb›_‹model›.png | |
| 2D plots of solution, name: Results/2D_plots/‹seq_name›_2Dsol‹guess_nb›_‹model›.png | |
| MATLBAL variables: Energy, Gradient, Hessian eigenvalues, Hessian condition number, Difference of the two obtained solutions |
Noy_339bp.m
| Inputs | bBDNA initial guesses read from 'Initial_guesses' folder |
| guesses must be named: | |
| Parameters | model for DNA: models "cgDNA+min" |
| sequence: range_guesses: list of ‹guess_nb› | |
| Outputs | 3D views of bBDNA solution, name: Results/3D_views/‹seq_name›_guess‹guess_nb›_‹model›.png |
| 3D views of bBDNAgd solution, name: Results/3D_views/‹seq_name›_3Dsol‹guess_nb›_‹model›.png | |
| 2D plots of solution, name: Results/2D_plots/‹seq_name›_2Dsol‹guess_nb›_‹model›.png | |
| 2D plots of solution, name: Results/2D_plots/‹seq_name›_2Dsol‹guess_nb›_‹model›.png | |
| MATLBAL variables: Energy, Gradient, Hessian eigenvalues, Hessian condition number, Difference of the two obtained solutions |
The script reads the stored variables of the computed solution and creates the figures.
The bBDNA software can be found on the LVCMM software page: link.