Elongation method for electronic structure calculations of random DNA sequences.
We applied ab initio order-N elongation (ELG) method to calculate electronic structures of various deoxyribonucleic acid (DNA) models. We aim to test potential application of the method for building a database of DNA electronic structures. The ELG method mimics polymerization reactions on a computer and meets the requirements for linear scaling computational efficiency and high accuracy, even for huge systems. As a benchmark test, we applied the method for calculations of various types of random sequenced A- and B-type DNA models with and without counterions. In each case, the ELG method maintained high accuracy with small errors in energy on the order of 10(-8) hartree/atom compared with conventional calculations. We demonstrate that the ELG method can provide valuable information such as stabilization energies and local densities of states for each DNA sequence. In addition, we discuss the "restarting" feature of the ELG method for constructing a database that exhaustively covers DNA species.
Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka, 816-8580, Japan.
Yuuichi
Y
Orimoto
Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka, 816-8580, Japan.
Kai
K
Liu
Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka, 816-8580, Japan.|Japan Science and Technology Agency, CREST, 4-1-8 Hon-Chou, Kawaguchi, Saitama, 332-0012, Japan.
Yuriko
Y
Aoki
D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004583:Electrons; D009690:Nucleic Acid Conformation; D011789:Quantum Theory
D004247:DNA
database; deoxyribonucleic acid; drug design; electronic structure; elongation method; library; material development; order-N [O(N)] method; random base pair sequence