Application of advanced graphics and fast computers is an important tool in the study of large molecular systems. It contributes considerably to the molecular level understanding of biomolecular structure and dynamics. The planned computational projects which will benefit great from the TITAN computer can be divided into two major categories: i. electronic structure calculations; ii. the dynamics of the nuclei on a given potential energy surface. To the first category belong the ab-initio studies of the influence of the environment on nucleotides and the calculation of ab-initio force fields of small biological molecules. The calculations are essential for the interpretation of the experimental results obtained in the groups of P. LeBreton and T. Keiderling. The study of nucleotides will be performed in conjunction with UV photoelectron spectroscopy, and the force field studies will help in quantifying the analysis of the Vibrational Circular Dichroism (VCD) results. To the second category belong the studies of the following subjects: i. ligand diffusion in hemoglobin, ii. the normal mode analysis of large biopolymers; iii. the Laplace inversion of light scattering data. In (i) a new simulation methodology will be developed to search on the molecular level of detail the diffusion coordinate of a ligand in hemoglobin. In (ii) the normal mode study of large biological molecules using empirical potentials will help in interpreting VCD spectra and will advance the theoretical foundation of the technique. In (iii) direct inversion of light scattering data will be performed. The above mentioned projects require high speed, large memory, and large mass storage which are not available at the university computational facilities. The dedicated machine is therefore essential to pursue the above studies.
| Czerminski, R; Elber, R (1991) Computational studies of ligand diffusion in globins: I. Leghemoglobin. Proteins 10:70-80 |
