Computational Interests - Selected programming work

Source code that I have developed in the framework of various projects.

1. A Molecular Dynamics program capable of simulating mixtures of various chain molecules of the form -(AXY-Bm)n where A and B are backbone atoms and X, Y are substituents. It is an offspring of an older program developed by prof. D. N. Theodorou and his coworkers; I have made numerous modifications and additions to meet my needs.

2. A Molecular Mechanics program that can build bulk systems of linear molecules of various molecular weights (united atom approximation).

3. A Bulk System Energy Optimization program, complementig the previous one. It decreases the energy and relaxes the structure of the systems generated by the Molecular Mechanics software, thus generating a more representative sample. A simple Monte Carlo scheme is employed instead of local algorithms, to better explore the configurational space.

4. A program to calculate pair distribution functions of bulk polymer systems and other geometric quantities of interest, using trajectories obtained via MD or MC.

5. Another program calculating diffusion coefficients by means of the well-known Einstein relation. It also generates information regarding anisotropy of diffusion. This is especially useful in studying motion of small penetrants travelling through slowly moving or completely fixed matrices like polymers or zeolites.

6. Velocity autocorrelation functions can be computed by this program if one wants to apply the Green-Kubo relations.

7. Time correlation functions of subchain end-to-end vector orientation and of dihedral angles are calculated here in order to obtain information about geometrical relaxation of polymer systems throughout simulation runs and relevant time scales.

8. Another program developed by prof. D. N. Theodorou's coworkers and subsequently modified by me: It calculates chemical potential solubility coefficients of short chain molecules inserted in a given matrix (Widom insertion method). A reference value is needed for the chemical potential and it is calculated by this program.

9. Various versions of a program calculating force-field parameters for a given molecule of the -(AXY-Bm)n type (see Nr 1 in this list), based on quantum mechanically optimized geometries and their energies.

10. Various versions of a program minimizing the force-field energy of a single molecule of the -(AXY-Bm)n type (see Nr 1 in this list); it is used as a tool complementing the previous program in order to develop new ab initio based force fields.

11. More software will be uploaded, hopefully soon, including programs to calculate various thermodynamic quantities of simulated systems, a single chain Monte Carlo code and a new method to detect jumps performed by penetrants travelling through slowly moving or fixed matrices, and treat them quantitatively. I apologize for the messy code and lack of documentation due to my limited time. Should you be interested, feel free to contact me.



Back to group members

Back to main page