Elongation method for electronic structure calculations of random DNA sequences

Yuuichi Orimoto, Kai Liu, Yuriko Aoki

    Research output: Contribution to journalArticlepeer-review

    7 Citations (Scopus)


    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.

    Original languageEnglish
    Pages (from-to)2103-2113
    Number of pages11
    JournalJournal of Computational Chemistry
    Issue number28
    Publication statusPublished - Oct 30 2015

    All Science Journal Classification (ASJC) codes

    • Chemistry(all)
    • Computational Mathematics


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