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- W92431749 abstract "A series of biomaterial related systems ― including water and DNA molecules ―have been studied using ab initio (first-principles) methods. By investigating the propertiesof water as the preliminary step, the hydrogen bond (HB) interactions, which play importantroles in biomolecules, were better understood from the quantum mechanical viewpoint. Thecalculated K-edge x-ray absorption near edge structure (XANES) spectra of all 340 oxygenatoms in the model have been accumulated to reproduce the experimental one. The spectrawere shown to be very sensitive to the HB configurations of O atoms, which could be used toelucidate the subtle structural variations in complex biomolecules. The simulation of singlemoleculeDNA overstretching experiments under torsionally constrained condition has beencarried out afterwards. The initial DNA models were stretched stepwisely and eventuallygained 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 indetails. 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 wasaccompanied by HB breaking and charge transfers. We have proposed an overstretched structure named O-DNA (Opened-DNA) to clarify the confusion in understanding thebehavior of DNA under high force load. With more experiences gained, a comprehensivemethodology revealing the underlying principles of bioprocesses from the quantummechanical viewpoint eventually come up. For the purpose of better computational accuracy,the scheme of implementing the generalized gradient approximation (GGA) exchangecorrelationfunctionals into the Orthogonalized Linear Combination of Atomic Orbitals(OLCAO) program suite has been discussed, and the computational efficiency has beenanalyzed correspondingly. Moreover, the parallel strategy for performing evaluation on aregular mesh and relevant updates to the file system were also presented. All the fundamentalworks above paved the way for more sophisticated study on wet DNA model and interfacesbetween biomolecules and bioceramic materials in the future." @default.
- W92431749 created "2016-06-24" @default.
- W92431749 creator A5070242749 @default.
- W92431749 date "2012-01-17" @default.
- W92431749 modified "2023-09-23" @default.
- W92431749 title "Ab initio computational applications to complex biomolecular systems" @default.
- W92431749 hasPublicationYear "2012" @default.
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