Elongation method for electronic structure calculations of random DNA sequences

Yuuichi Orimoto, Kai Liu, Yuriko Aoki

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

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
Volume36
Issue number28
DOIs
Publication statusPublished - Oct 30 2015

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Electronic Structure
Elongation
Electronic structure
DNA
High Accuracy
Computational efficiency
Stabilization
Polymerization
Density of States
Energy
Computational Efficiency
Atoms
Scaling
Cover
Benchmark
Calculate
Requirements
Model
Demonstrate

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Computational Mathematics

Cite this

Elongation method for electronic structure calculations of random DNA sequences. / Orimoto, Yuuichi; Liu, Kai; Aoki, Yuriko.

In: Journal of Computational Chemistry, Vol. 36, No. 28, 30.10.2015, p. 2103-2113.

Research output: Contribution to journalArticle

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