This page lists the references relevant for Conquest, gives brief descriptions of each paper, contains links to on-line journals and also has PDF versions of preprints. This list is ordered by year of publication.


  • “Structural analysis based on unsupervised learning: Search for a characteristic low-dimensional space by local structures in atomistic simulations”, Ryo Tamura, Momo Matsuda, Jianbo Lin, Yasunori Futamura, Tetsuya Sakurai, and Tsuyoshi Miyazaki, Phys. Reg. B 105, 075107 (2022) DOI:10.1103/PhysRevB.105.075107


  • “Origin of Ferroelectric Domain Wall Alignment with Surface Trenches in Ultrathin Films”, J. S. Baker and D. R. Bowler, Phys. Rev. Lett. 127, 247601 (2021) DOI:10.1103/PhysRevLett.127.247601

  • “The investigation of methane storage at the Ni-MOF-74 material: a periodic DFT calculation”, Chen-Hao Yeh, Abdul Hannan Khan, Tsuyoshi Miyazaki and Jyh-Chiang Jiang, Phys. Chem. Chem. Phys. 23, 12270 (2021) DOI:10.1039/D1CP01276B

  • “The Emergence of Multiple Coordination Numbers in Gold–Cyanoarene Complexes: A Study of the On-Surface Coordination Mechanism”, Waka Nakanishi, Ayako Nakata, Paola Perez, Masayuki Takeuchi, Christian Joachim, and Keisuke Sagisaka, J. Phys. Chem. C 125, 9937 (2021) DOI:10.1021/acs.jpcc.1c02456

  • “Air-Stable and Reusable Cobalt Phosphide Nanoalloy Catalyst for Selective Hydrogenation of Furfural Derivatives”, Hiroya Ishikawa, Min Sheng, Ayako Nakata, Kiyotaka Nakajima, Seiji Yamazoe, Jun Yamasaki, Sho Yamaguchi, Tomoo Mizugaki, and Takato Mitsudome, ACS Catal. 11, 750 (2021) DOI:10.1021/acscatal.0c03300


  • “Structural change of damaged polyethylene by beta-decay of substituted tritium using reactive force field”, Haolun Li, Susumu Fujiwara, Hiroaki Nakamura, Tomoko Mizuguchi, Ayako Nakata, Tsuyoshi Miyazaki and Shinji Saito, Jpn. J. Appl. Phys. 60, SAAB06 (2020) DOI:10.35848/1347-4065/abbdc8

  • “First-principles study of topologically protected vortices and ferroelectric domain walls in hexagonal YGaO3”, Didrik R. Småbråten, Ayako Nakata, Dennis Meier, Tsuyoshi Miyazaki, and Sverre M. Selbach, Phys. Rev. B 102, 144103 (2020) DOI:10.1103/PhysRevB.102.144103

  • “Notes on density matrix perturbation theory”, L. A. Truflandier, R. M. Dianzinga and D. R. Bowler, J. Chem. Phys. 153, 164105 (2020) DOI:10.1063/5.0022244

  • “Polar Morphologies from First Principles: PbTiO3 Films on SrTiO3 Substrates and the p(2×Λ) Surface Reconstruction”, J. S. Baker and D. R. Bowler, Adv. Theory Simul. 3, 2000154 (2020) DOI:10.1002/adts.202000154

  • “Blue moon ensemble simulation of aquation free energy profiles applied to mono and bifunctional platinum anticancer drugs”, T. Hirakawa, D. R. Bowler, T. Miyazaki, Y. Morikawa and L. A. Truflandier, J. Comput. Chem. 41, 1973 (2020) DOI:10.1002/jcc.26367

  • “The pseudoatomic orbital basis: electronic accuracy and soft-mode distortions in ABO3 perovskites”, J. S. Baker, T. Miyazaki and D. R. Bowler, Electron. Struct. 2, 025002 (2020) DOI:10.1088/2516-1075/ab950e

  • “A cobalt phosphide catalyst for the hydrogenation of nitriles”, Takato Mitsudome, Min Sheng, Ayako Nakata, Jun Yamasaki, Tomoo Mizugaki and Koichiro Jitsukawa, Chem. Sci., 11, 6682 (2020) DOI:10.1039/D0SC00247J

  • “Large scale and linear scaling DFT with the CONQUEST code”, A. Nakata, J. S. Baker, S. Y. Mujahed, J. T. L. Poulton, S. Arapan, J. Lin, Z. Raza, S. Yadav, L. Truflandier, T. Miyazaki and D. R. Bowler, J. Chem. Phys. 152, 164112 (2020) DOI:10.1063/5.0005074


  • “Highly accurate local basis sets for large-scale DFT calculations in CONQUEST”, D. R. Bowler, J. S. Baker, J. T. L. Poulton, S. Y. Mujahed, J. Lin, S. Yadav, Z. Raza and T. Miyazaki, Jap. J. Appl. Phys. 58, 100503 (2019) DOI:10.7567/1347-4065/ab45af

  • “DFT study of undoped and As-doped Si nanowires approaching the bulk limit”, C. Kumarasinghe and D. R. Bowler, J. Phys.: Condens. Matter 32, 035304 (2019) DOI:10.1088/1361-648x/ab4b3c

  • “Gate controlling of quantum interference and direct observation of anti-resonances in single molecule charge transport”, Y. Li, M. Buerkle, G. Li, A. Rostamian, H. Wang, Z. Wang, D. R. Bowler, T. Miyazaki, L. Xiang, Y. Asai, G. Zhou and N. Tao, Nature Mater. 18, 357 (2019) DOI:10.1038/s41563-018-0280-5


  • “Structural properties of silicon–germanium and germanium–silicon core–shell nanowires”, C. O’Rourke, S. Y. Mujahed, C. Kumarasinghe, T. Miyazaki and D. R. Bowler, J. Phys.: Condens. Matter 30 465303 (2018) DOI:10.1088/1361-648X/aae617
  • “High-accuracy large-scale DFT calculations using localized orbitals in complex electronic systems: the case of graphene–metal interfaces”, C. Romero-Muñiz, A. Nakata, P. Pou, D. R. Bowler, T. Miyazaki and R. Pérez, J. Phys.: Condens. Matter 30 505901 (2018) DOI:10.1088/1361-648X/aaec4c


  • “Efficient Calculation of Electronic Structure Using O(N) Density Functional Theory”, A. Nakata, Y. Futamura, T. Sakurai, D. R. Bowler and T. Miyazaki, J. Chem. Theory Comput. 13 4146 (2017) DOI:10.1021/acs.jctc.7b00385
  • “Canonical-ensemble extended Lagrangian Born–Oppenheimer molecular dynamics for the linear scaling density functional theory”, T. Hirakawa, T. Suzuki, D. R. Bowler and T. Miyazaki, J. Phys.: Condens. Matter 29 405901 (2017) DOI:10.1088/1361-648X/aa810d


  • “Communication: Generalized canonical purification for density matrix minimization”, L. A. Truflandier, R. M. Dianzinga and D. R. Bowler, J. Chem. Phys. 144, 091102 (2016) DOI:10.1063/1.4943213
  • “Linear-scaling first-principles molecular dynamics of complex biological systems with the Conquest code”, T. Otsuka, M. Taiji, D. R. Bowler and T. Miyazaki, Jap. J. Appl. Phys. 55,  1102B1  (2016) DOI:10.7567/JJAP.55.1102B1


  • “Linear scaling density matrix real time TDDFT: Propagator unitarity and matrix truncation”, C. O’Rourke and D. R. Bowler, J. Chem. Phys. 143, 102801 (2015) DOI:10.1063/1.4919128
  • “Optimized multi-site local orbitals in the large-scale DFT program CONQUEST”, A. Nakata, D. Bowler and T. Miyazaki, Phys. Chem. Chem. Phys.  17,  31427  (2015) DOI:10.1039/C5CP00934K


  • “Stable and Efficient Linear Scaling First-Principles Molecular Dynamics for 10,000+ atoms”, M. Arita, D. R. Bowler and T. Miyazaki, J. Chem. Theory Comput. 10 5419 (2014) DOI:10.1021/ct500847y
  • “Large-scale DFT simulations with a linear-scaling DFT code CONQUEST on K-computer”, M. Arita, S. Arapan, D. R. Bowler and T. Miyazaki, J. Adv. Simul. Sci. Eng.  1, 87 (2014) DOI:10.15748/jasse.1.87
  • “Efficient Calculations with Multisite Local Orbitals in a Large-Scale DFT Code CONQUEST”, A. Nakata, D. R. Bowler and T. Miyazaki, J. Chem. Theory Comput. 10, 4813  (2014) DOI:10.1021/ct5004934


  • “Density-functional theory study of gramicidin A ion channel geometry and electronic properties”, M. Todorović, D. R. Bowler, M. J. Gillan, T. Miyazaki, J. R. Soc. Interface 10, 20130547 (2013). DOI:10.1098/rsif.2013.0547 Paper studying the electrostatic potential in the gramicidin A channel


  • “O(N) methods in electronic structure calculations”, D. R. Bowler and T. Miyazaki, Rep. Prog. Phys. 75, 036503 (2012). DOI:10.1088/0034-4885/75/3/036503 Exhaustive review of linear scaling methods.


  • “Linear Scaling Constrained Density Functional Theory in CONQUEST”, A. M. P. Sena, T. Miyazaki and D. R. Bowler, J. Chem. Theory Comput. 7, 884 (2011). DOI:10.1021/ct100601n Paper detailing the implementation of constrained DFT in Conquest.


  • “Calculations for millions of atoms with density functional theory: linear scaling shows its potential”, D. R. Bowler and T. Miyazaki, J. Phys.: Condens. Matter 22, 074207 (2010). DOI:10.1088/0953-8984/22/7/074207 Paper demonstrating that DFT calculations on systems containing millions of atoms are now possible.


  • “Non-self-consistent Density-Functional Theory Exchange-Correlation Forces for GGA Functionals”, A. S. Torralba, D. R. Bowler, T. Miyazaki and M. J. Gillan, J. Chem. Theory Comput. 5, 1499 (2009). DOI:10.1021/ct8005425 Implementation of GGA in Conquest both self-consistently and non-self-consistently.


  • “The energetics of hut-cluster self-assembly in Ge/Si(001) from linear-scaling DFT calculations”, T. Miyazaki, D. R. Bowler, M. J. Gillan and T. Ohno, J. Phys. Soc. Jpn. 77, 123706 (2008). DOI:10.1143/JPSJ.77.123706 Studying self-assembled hut clusters of Ge on Si(001) with system sizes up to 23,000 atoms.
  • “Accuracy of order-N density-functional theory calculations on DNA systems using CONQUEST”, T. Otsuka, T. Miyazaki, T. Ohno, D. R. Bowler and M. J. Gillan, J. Phys.:Condens. Matter 20, 294201 (2008). DOI:10.1088/0953-8984/20/29/294201 A study of DNA fragments (up to 10 base-pairs) with Conquest.
  • “Pseudo-atomic orbitals as basis sets for the O(N) DFT code CONQUEST”, A. S. Torralba, M. Todorovic, V. Brazdova, R. Choudhury, T. Miyazaki, M. J. Gillan and D. R. Bowler, J. Phys.:Condens. Matter 20, 294206 (2008). DOI:10.1088/0953-8984/20/29/294206 Description of the PAO implementation in Conquest, including an important result about symmetry.
  • “Automatic data distribution and load balancing with space-filling curves: implementation in CONQUEST”, V. Brazdova and D. R. Bowler, J. Phys.: Condens. Matter 20, 275223 (2008). DOI:0.1088/0953-8984/20/27/275223 Details of one of the load-balancing schemes used in Conquest.


  • “Density functional calculations of Ge(105): Local basis sets and O(N) methods”, T. Miyazaki, D. R. Bowler, R. Choudhury and M. J. Gillan, Phys. Rev. B 76, 115327 (2007). DOI:10.1103/PhysRevB.76.115327 Investigation of Ge(105) surface using Conquest.
  • “Order-N first-principles calculations with the CONQUEST code”, M. J. Gillan, D. R. Bowler, A. S. Torralba and T. Miyazaki, Comp. Phys. Commun. 177, 14 (2007). DOI:10.1016/j.cpc.2007.02.075 Overview of recent developments and applications of Conquest.


  • “Recent progress with large-scale ab initio calculations: the CONQUEST code”, D. R. Bowler, R. Choudhury, M. J. Gillan and T. Miyazaki, phys. stat. sol. b 243, 989 (2006). DOI:10.1002/pssb.200541386 Overview of linear scaling methods, together with a description of recent developments and applications of Conquest.
  • “Large-scale ab-initio calculations”, T. Miyazaki, R. Choudhury, D. R. Bowler and M. J. Gillan, Proc. of 3rd Int. Conf. on Comput. Model. and Simul. of Materials, ed. P. Vincenzini. (Techna Group, Faenza, Italy, 2005). Local copy of preprint in PDF. Presentation of forces and relaxation of Si(001) in Conquest.
  • “Atomic force algorithms in DFT electronic-structure techniques based on local orbitals”, T. Miyazaki, D. R. Bowler, R. Choudhury and M. J. Gillan, Journal of Chemical Physics 121, 6186 (2004). DOI:10.1063/1.1787832 Details of implementation of atomic forces for DFT techniques using localised orbitals.
  • “Recent progress in linear scaling ab initio electronic structure techniques”, D. R. Bowler, T. Miyazaki and M. J. Gillan, Journal of Physics:Condensed Matter 14 , 2781 (2002). DOI:10.1088/0953-8984/14/11/303 General overview of linear scaling methods and Conquest in particular.
  • “An embedding scheme based on quantum linear-scaling methods”, D. R. Bowler and M. J. Gillan, Chemical Physics Letters 355 , 306 (2002). DOI:10.1016/S0009-2614(02)00273-7 An implementation of embedding using the O(N) method within Conquest.
  • “Parallel Sparse Matrix Multiplication for Linear Scaling Electronic Structure Calculations”, D. R. Bowler, T. Miyazaki and M. J. Gillan, Computer Physics Communications 137 , 255 (2001). DOI:10.1016/S0010-4655(01)00164-3 Detailed description and tests of sparse matrix multiplication for parallel computers as implemented in Conquest.


  • “Practical methods for ab initio calculations on thousands of atoms”, D. R. Bowler, I. J. Bush and M. J. Gillan, International Journal of Quantum Chemistry, 77 , 831 (2000). DOI:10.1002/(SICI)1097-461X(2000)77:5<831::AID-QUA5>3.0.CO;2-G Early overview of Conquest.
  • “Density matrices in O(N) electronic structure calculations: theory and applications”, D. R. Bowler and M. J. Gillan, Computer Physics Communications 120 , 95 (1999). DOI:10.1016/S0010-4655(99)00221-0 How to achieve a robust linear scaling method by combining McWeeny iteration with the auxiliary density matrix method. This is the linear scaling solver currently implemented in Conquest.
  • “Length-scale ill conditioning in linear-scaling DFT”, D. R. Bowler and M. J. Gillan, Computer Physics Communications 112 , 103 (1998). DOI:10.1016/S0010-4655(98)00061-7 Description of simplest form of ill-conditioning involved in minimising energy with respect to support functions (particularly in the context of blip functions as a basis).
  • “First Principles Order N Calculations on Very Large Systems”, M. J. Gillan, D. R. Bowler, C. M. Goringe and E. Hernandez, in ‘‘The Physics of Complex Liquids’’, Proceedings of the Internationl Symposium, 10-12 November 1997, Nagoya, Japan, ed. F. Yonezawa, K. Tsuji, K. Kaji, M. Doi and T. Fujiwara (World Scientific, 1998). Local copy of preprint in PDF. Discussion of three forms of ill-conditioning affecting localised basis techniques.
  • “Linear-scaling DFT-pseudopotential calculations on parallel computers”, C. M. Goringe, E. Hernandez, M. J. Gillan and I. J. Bush, Computer Physics Communications 102, 1 (1997). DOI:10.1016/S0010-4655(97)00029-5 Description of parallelisation of the Conquest code in its original form.
  • “Basis functions for linear-scaling first-principles calculations”, E. Hernandez, M. J. Gillan and C. M. Goringe, Physical Review B 55, 13485 (1997). DOI:10.1103/PhysRevB.55.13485 Description of the B-spline basis set used in the Conquest code.
  • “Linear-scaling density-functional-theory technique: The density-matrix approach”, E. Hernandez, M. J. Gillan and C. M. Goringe, Physical Review B 53, 7147 (1996). DOI:10.1103/PhysRevB.53.7147 Detailed description of the implementation of the practical linear scaling DFT code, Conquest.
  • “Self-consistent first-principles technique with linear scaling”, E. Hernandez and M. J. Gillan, Physical Review B 51, 10157 (1995). DOI:10.1103/PhysRevB.51.10157 Paper describing the strategy used to achieve practical linear scaling performance in Conquest DFT calculations.