Partition function calculations for DNA using the Transfer Matrix Method.
- Linux OS
- Mathematica (data analysis)
- GCC 4.7
- OpenMP
- GSL Scientific Library
Run the script COMPILE.sh to compile. This will create a new binary file called Nucleation with the older file being renamed to Nucleation.bak (If a binary file already exists). The source code and makefile are located in the ./src directory.
The table highlights the parameters needed to run the calculations
| Parameter | Cmd Flag | Type | Notes |
|---|---|---|---|
| L | --L | <int> or <double> | Specifies the range of dimensionless space |
| m | --m | <int> | Sets the delta |
| N | --N | <int> | Sets the number of base-pairs in the structure |
| eta_b | --eta_b | <double> | Sets the elastic range in the potential |
| kappa | --kappa | <double> | Sets the spring constant of the backbones |
| sigma | --sigma | <double> | Sets the spring constant of the base-pairs |
| umin | --umin | <int> | Starting position of the extension (number of delta's) |
| umax | --umax | <int> | End position of the extension (number of delta's) |
There are two methods to run the calculations. The first method involves running the binary file from the command line
$ ./Nucleation
This will initiate a user interface asking for parameters needed for the calculations. The second method bypasses the user interface and allows the passing of parameters from execution
$ ./Nucleation --L <INT> --m <INT> --N <INT> --eta_b <DOUBLE> --kappa <DOUBLE> --sigma <DOUBLE> --umin <INT> --umax <INT>
Results from the calculations are written to the directory ./results categorised into sub-directories for each state (Intact, Frayed and Bubble). After the results are generated run the mathematica books in the directories to perform the analysis and plots.