Ab initio computational applications to complex biomolecular systems
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A series of biomaterial related systems ― including water and DNA molecules ― have been studied using ab initio (first-principles) methods. By investigating the properties of water as the preliminary step, the hydrogen bond (HB) interactions, which play important roles in biomolecules, were better understood from the quantum mechanical viewpoint. The calculated K-edge x-ray absorption near edge structure (XANES) spectra of all 340 oxygen atoms in the model have been accumulated to reproduce the experimental one. The spectra were shown to be very sensitive to the HB configurations of O atoms, which could be used to elucidate the subtle structural variations in complex biomolecules. The simulation of singlemolecule DNA overstretching experiments under torsionally constrained condition has been carried out afterwards. The initial DNA models were stretched stepwisely and eventually gained an extension of 1.5-fold (150% × the original length). The variation of total energy, atomic configuration, and the electronic structure during this process were analyzed in details. At the extension of ~1.3-fold, the ring opening reactions occurred in the backbones. The backbone nicks appeared at elongations of ~1.40-fold. The whole process was accompanied by HB breaking and charge transfers. We have proposed an overstretched structure named O-DNA (Opened-DNA) to clarify the confusion in understanding the behavior of DNA under high force load. With more experiences gained, a comprehensive methodology revealing the underlying principles of bioprocesses from the quantum mechanical viewpoint eventually come up. For the purpose of better computational accuracy, the scheme of implementing the generalized gradient approximation (GGA) exchangecorrelation functionals into the Orthogonalized Linear Combination of Atomic Orbitals (OLCAO) program suite has been discussed, and the computational efficiency has been analyzed correspondingly. Moreover, the parallel strategy for performing evaluation on a regular mesh and relevant updates to the file system were also presented. All the fundamental works above paved the way for more sophisticated study on wet DNA model and interfaces between biomolecules and bioceramic materials in the future.
Table of Contents
Introduction -- Theoretical methods -- Case studies -- Future work -- Appendix A. VASP relaxation running time comparison -- Appendix B. Typical initial datasets of oxygen atomic orbitals -- Appendix D. Abbreviaitons