Code for making chapter 2 results of my thesis making the fine grained systems using an absorption matrix
2 monomer system of right(0) and wrong(1)
To run on the cluster :
- g++ -lboost_program_options 230412_model_big_abs_matrix_differentX_grow_mRNA_wr_energetic_beginww.cpp -o Muriel
- change 230131_read_parameters_models.py
- change run_model.sh
- qsub run_model.sh
Paramaters:
`bool all_steps = false`; -> can be removed I think
`bool multiple_DNA = true`;
-> if false: Makes files for every polymer made describing all transitions, e.g did the system add a monomer (0 or 1) or did the ystem move back removing the current monomer tip.
-> if true: makes one file of every polymer made describing only the end polymer and the error probability of that polymer.
`string DIR = "230714output"`;- -> directory where it puts the files
`string x_def = "1"`; --> x definition of the polymerisation step
`string M_model = "MB2"`; -> fine grained model used (MB2 = BF, MB1 = BB, MF2 = FF, MF1 = FB)
`int number_steps = 30`; -> number of polymers simulated
`int length_mRNA = 300`; -> length of ervey polymer that is siumlated
`bool variables_in_main = false`;
-> if false: run script on your computer
-> if true run the script on cluster Then aslo comment out the upper section of the code and comment in the section where i define parameters using external files (needed for cluster)
`vector<double> L_delta_g_tt = {3,5}`; --> delta g_tt = Delta G_r - Delta G_w: parameter defining copy/template interactions
`vector<double> L_delta_g_pol = {0,1,2,3,4,5,6,7,8,9,10}`; --> Delta G_bb: backbone strength variation
Code for makring chapter 2 of my thesis making the fully computational model
2 monomer system: right(0) wrong(1)
- g++ -lboost_program_options 230412_grow_mRNA_wr_energetic_without_absorption_matrix_beginw.cpp -o no_abs
- change 230131_read_parameters_models.py
- change run_model.sh
- qsub run_model.sh
Paramaters te same as for 230412_model_big_abs_matrix_differentX_grow_mRNA_wr_energetic_beginww.cpp
Code for results chapter 3 + 4
4 nucleotide system of polymer copying
To run on the cluster :
- g++ -lboost_program_options 230526_Big_abs_BF_x1_4differentbases_with_pupu_pypy_coststep13.cpp -o 4_bases
- change 230413_read_parameters_4bases_forloop.py
- change run_model_4bases.sh
- qsub run_model_4bases.sh
Paramaters:
`bool variables_in_main =true`;
-> if false: run script on your computer
-> if true run the script on cluster Then aslo comment out the upper section of the code and comment in the section where i define parameters using external files (needed for cluster)
`string DIR = "";` = ("DIR", po::value<string>(), "output directory name") --> directory for output files
`bool multiple_DNA`; = ("multiple_DNA", po::value<bool>(), "compute multiple DNA string")
-> if false: Makes files for every polymer made describing all transitions, e.g did the system add a monomer (0 or 1) or did the ystem move back removing the current monomer tip.
-> if true: makes one file of every polymer made describing only the end polymer and the error probability of that polymer.
`int number_steps`; = ("number_DNA", po::value<int>(), "number of DNA computed") --> number of polymer string made
`string x_def = ""`; = ("x_def", po::value<string>(), "strength x, backbone") --> x definition of polymerisation step, b+ and b-
`int length_mRNA`; = ("mRNA_length", po::value<int>(), "length of the mRNA string formed") -> length of polymers computed
`vector<double> L_delta_g_pol`; = ("L_g_pol", po::value< vector<double> >(), "delta G_pol definitions list") -> Delta G_bb: backbone strength variation
`vector<double> ratio_bases_template`; = ("ratio_template", po::value< vector<double> >(), "the ratio of the four bases we are using") --> ratio of purine1,purine2, pyrimidn1 and pyrimdine2 on template
`string purine_1` = ""; = ("purine_1", po::value<string>(), "purine 1 base definition") --> which purine used
`string purine_2` = ""; = ("purine_2", po::value<string>(), "purine 2 base definition") -->which purine used
`string pyrimidines_1` = ""; = ("pyrimidines_1", po::value<string>(), "pyrimidines 1 base definition") --> which pyrimidine used, complementary to purine1
`string pyrimidines_2` = ""; = ("pyrimidines_2", po::value<string>(), "pyrimidines 2 base definition") --> which pyrimidine used, complementary to purine2
`int repulsion_00_11`; = ("repulsion_11_00", po::value<int>(), "strength repulsion purine-pruine or pyrimidine-pyrimidine binding") --> \Delta G_{cost}
4 nucleotide system of polymer copying putting the cost on b+
Code for theoretical result 6 nucleotide alphabet: conclusion and outlook chapter of thesis
Note that all fine grained models of 6 nucleotides do not work --> they do not give the right results yes
For running or 2 monomer system codes
For running all codes with 4 or 6 bases
absoption matrix of the simplified system of figure 8
Big absoption matrix(figure 21, thesis) for 4 bases system
Big absoption matrix(figure 21, thesis) but then for 6 bases instead of 4
absoption matrix of system of 4 bases in the limit of inifite backbone strength (figure 12 of thesis) with x=1
absoption matrix of system of 6 bases in the limit of inifite backbone strength with x=1
Absorption matrix of system chapter 2 in the limit of infinite backbone strength((figure 12 of thesis) with x can be varied