Skylaris Group
Computational Chemistry

Group publications

Papers in Journals

• Rhodium(I) complexes containing the enolate of N-acetyl-3-butanoyltetramic acid and the crystal structure of [Rh(abta){P(OPh)3}2] . B. T. Heaton, C. Jacob, J. Markopoulos, O. Markopoulou, J. Nahring, C.-K. Skylaris and A. K. Smith. J. Chem. Soc., Dalton Trans. (1996) 1701.
• A two-centre implementation of the Douglas-Kroll transformation in relativistic calculations. L. Gagliardi, N. C. Handy, A. G. Ioannou, C.-K. Skylaris, S. Spencer, A. Willetts and A. M. Simper. Chem. Phys. Lett. 283 (1998) 187. ( pdf )
• An efficient method for calculating effective core potential integrals which involve projection operators. C.-K. Skylaris, L. Gagliardi, N. C. Handy, A. G. Ioannou, S. Spencer, A. Willetts and A. M. Simper. Chem. Phys. Lett. 296 (1998) 445. ( pdf )
• A Relativistic Density Functional Study on the Uranium Hexafluoride and Plutonium Hexafluoride Monomer and Dimer Species. L. Gagliardi, A. Willetts, C.-K. Skylaris, N. C. Handy, S. Spencer, A. G. Ioannou and A. M. Simper. J. Am. Chem. Soc. 120 (1998) 11727. ( pdf ) ( ps.gz )
• A theoretical study of plutonium diketone complexes for solvent extraction. L. Gagliardi, N. C. Handy, C.-K. Skylaris and A. Willetts. Chem. Phys. 252 (2000) 47. ( ps.gz )
• MAGIC: An Integrated Computational Environment for the modelling of heavy atom Chemistry. A. Willetts, L. Gagliardi, A. G. Ioannou, A. M. Simper, C.-K. Skylaris, S. Spencer and N. C. Handy. Int. Rev. Phys. Chem. (2000). 19(3) (2000) 327. ( pdf ) ( abstract )
• The Hydration of UO2(2+) and PuO2(2+). S. Spencer, L. Gagliardi, N. C. Handy, A. G. Ioannou, C.-K. Skylaris, A. Willetts and A. M. Simper. J. Phys. Chem. A 103(12) (1999) 1831. ( pdf )
• Extensions on the parallel version of the MAGIC program. C.-K. Skylaris. Flying High: News from CINECA's ICARUS project. 16-17 (1999) 2.
• On the Resolution of Identity Coulomb energy approximation in Density Functional Theory. C.-K. Skylaris, L. Gagliardi, N. C. Handy, A. G. Ioannou, S. Spencer and A. Willetts. J. Mol. Struct.: Theochem. 501-502 (2000) 229. (pdf)( ps.gz )
• A density functional study of thorium tetrahalides. L. Gagliardi, C.-K. Skylaris, A. Willetts, J. M. Dyke and V. Barone. Phys. Chem. Chem. Phys. 2 (2000) 3111. ( pdf ) ( ps.gz )
• Accurate kinetic energy evaluation in electronic structure calculations with localized functions on real space grids. C.-K. Skylaris, A. A. Mostofi, P. D. Haynes, C. J. Pickard and M. C. Payne. Comput. Phys. Commun.140 (3) (2001) 315.( pdf )
• The Non-orthogonal Generalised Wannier Function pseudopotential plane-wave method. C.-K. Skylaris, A. A. Mostofi, P. D. Haynes, O. Dieguez and M. C. Payne. Phys. Rev. B 66 (2002) 035119 ( pdf ) ( ps.gz ).
• Comparison of variational real-space representations of the kinetic energy operator. C.-K. Skylaris, O. Dieguez, P. D. Haynes and M. C. Payne. Phys. Rev. B 66 (2002) 073103 ( pdf ) ( ps.gz ).
• Total-energy calculations with localised functions and plane waves. A. A. Mostofi, C.-K. Skylaris, P. D. Haynes and M. C. Payne. Comput. Phys. Commun. 147 (2002) 788 ( pdf ).
• Density functional and ab initio study of the tautomeric forms of 3-acetyl tetronic and 3-acetyl tetramic acids. C.-K. Skylaris, O. Igglessi-Markopoulou, A. Detsi and J. Markopoulos. Chemical Physics. 293 (2003) 355 ( pdf ).
• Cyclisation of novel amino oxo esters to tetramic Acids - Density functional theory study of the reaction mechanism. A. Detsi, A. Afantitis, G. Athanasellis, J. Markopoulos, O. Igglessi-Markopoulou and C.-K. Skylaris. Eur. J. Org. Chem. (2003) 4593 ( pdf ).
• Preconditioned iterative minimisation for linear-scaling electronic structure calculations. A. A. Mostofi, P. D. Haynes, C.-K. Skylaris and M. C. Payne. J. Chem. Phys. 119(17) (2003) 8842 ( pdf ).
• Introducing ONETEP: Linear-scaling density functional simulations on parallel computers. C.-K. Skylaris, P. D. Haynes, A. A. Mostofi and M. C. Payne. J. Chem. Phys. 122 (2005) 084119 ( pdf ).
• Using ONETEP for accurate and efficient O(N) density functional calculations. C.-K. Skylaris, P. D. Haynes, A. A. Mostofi and M. C. Payne. J. Phys.: Condens. Matter. 17 (2005) 5757 ( pdf ).
• Torsional unharmonicity in the conformational analysis of beta-D-galactose. Y. K. Sturdy, C.-K. Skylaris and D. C. Clary. J. Phys. Chem. B. 110 (2006) 3485 ( pdf ).
• Implementation of linear-scaling plane wave density functional theory on parallel computers. C.-K. Skylaris, P. D. Haynes, A. A. Mostofi and M. C. Payne. Phys. Stat. Sol. (b). 243(5) (2006) 973 ( pdf ).
• ONETEP: linear-scaling density-functional theory with local orbitals and plane waves. P. D. Haynes, C.-K. Skylaris, A. A. Mostofi and M. C. Payne. Phys. Stat. Sol. (b). 243(11) (2006) 2489 ( pdf ).
• ONETEP: linear-scaling density-functional theory with plane waves. P. D. Haynes, A. A. Mostofi, C.-K. Skylaris and M. C. Payne. J. Phys.: Conf. Ser. 26 (2006) 143 ( pdf ).
• Elimination of basis set superposition error in linear-scaling density-functional calculations with local orbitals optimised in situ. P. D. Haynes, C.- K. Skylaris, A. A. Mostofi and M. C. Payne. Chem. Phys. Lett. 422 (2006) 345 ( pdf ).
• Novel structural features of CDK inhibition revealed by an ab initio computational method combined with dynamic simulations. L. Heady, M. Fernandez-Serra, R. L. Mancera, S. Joyce, A. R. Venkitaraman, E. Artacho, C.-K. Skylaris, L. Colombi Ciacchi and M. C. Payne. J. Med. Chem. 49 (2006) 5141( pdf ).
• Achieving plane wave accuracy in linear-scaling density functional theory applied to periodic systems: A case study on crystalline silicon. C.-K. Skylaris and P. D. Haynes. J. Chem. Phys. 127 (2007) 164712 ( pdf ).
• Recent progress in linear-scaling density functional calculations with plane waves and pseudopotentials: the ONETEP code. C.-K. Skylaris, P. D. Haynes, A. A. Mostofi and M. C. Payne. J. Phys. Condens. Matter 20 (2008) 064209 ( pdf ).
• Density kernel optimisation in the ONETEP code. P. D. Haynes, C.-K. Skylaris, A. A. Mostofi and M. C. Payne. J. Phys. Condens. Matter 20 (2008) 294207 ( pdf ).
• Classical molecular dynamics simulations of the complex between the RAD51 protein and the BRC hairpin loops of the BRCA2 protein. N. Buis, C.-K. Skylaris, G. H. Grant, E. Rajendra, M. C. Payne, and A. R. Venkitaraman. Mol. Sim. 34 (2008) 749 ( pdf ).
• Including dispersion interactions in the ONETEP program for linear-scaling density functional theory calculations. Q. Hill and C.-K. Skylaris. Proc. R. Soc. A 465 (2009) 669 ( pdf ).
• Linear-scaling density-functional theory with tens of thousands of atoms: Expanding the scope and scale of calculations with ONETEP. N. D. M. Hine, P. D. Haynes, A. A. Mostofi, C.-K. Skylaris and M. C. Payne, Comput. Phys. Comm. 180 (2009) 1041 ( pdf ).
• Large-scale first principles and tight-binding density functional theory calculations on hydrogen-passivated silicon nanorods. N. Zonias, P. Lagoudakis and C.-K. Skylaris. J. Phys.: Condens. Matter 22 (2010) 025303 ( pdf ).
• Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations. D. J. Cole, C.-K. Skylaris, E. Rajendra, A. R. Venkitaraman and M. C. Payne. Europhysics Letters 91 (2010) 37004 ( pdf ).
• Computational prediction of L3 EXAFS spectra of gold nanoparticles from classical Molecular Dynamics simulations. O. M. Roscioni, N. Zonias, S. W. T. Price, A. E. Russell, T. Comaschi, and C.-K. Skylaris. Phys. Rev. B 83 (2011) 115409 ( pdf ).
• First principles-based calculations of free energy of binding: application to ligand-binding in a self-assembling superstructure S. Fox, H. Wallnoefer, T. Fox, C. Tautermann , and C.-K. Skylaris. J. Chem. Theor. Comput. 7 (2011) 1102 ( pdf ).
• Accurate ionic forces and geometry optimisation in linear scaling density-functional theory with local orbitals. N. D. M. Hine, M. Robinson, Peter D. Haynes C.-K. Skylaris, M. C. Payne and A. A. Mostofi. Phys. Rev. B 83 (2011) 195102 ( pdf ).
• Interrogation of the Protein-Protein Interactions between Human BRCA2 BRC Repeats and RAD51 Reveals Atomistic Determinants of Affinity. D. J. Cole, E. Rajendra, M. Roberts-Thomson, B. Hardwick, G. J. McKenzie, M. C. Payne, A. R. Venkitaraman and C.-K. Skylaris. PLoS Computational Biology 7 (2011) e1002096 ( pdf ).
• Minimal parameter implicit solvent model for ab initio electronic structure calculations. J. Dziedzic, H. H. Helal, C.-K. Skylaris, A. A. Mostofi, and M. C. Payne. Europhysics Letters 95 (2011) 43001 ( pdf ) .
• Electrostatic interactions in finite systems treated with periodic boundary conditions: Application to linear-scaling density functional theory. N. D. M. Hine, J. Dziedzic, P. D. Haynes, and C.-K. Skylaris. J. Chem. Phys. 135 (2011) 204103 ( pdf ) .
• Electrostatic embedding in large-scale first principles quantum mechanical calculations on biomolecules. S. J. Fox., C. Pittock, T. Fox, C. Tautermann, N. Malcolm, and C.-K. Skylaris. J. Chem. Phys. 135 (2011) 224107 ( pdf ) .
• Fitting EXAFS data using molecular dynamics outputs and a histogram approach. S. W. T. Price, N. Zonias, C.-K. Skylaris, T. I. Hyde, B. Ravel and A. E. Russell. Submitted (2011) .
• Natural Bond Orbital Analysis in Linear-Scaling Density Functional Theory Calculations: application to a protein-protein interface. L. P. Lee, D. J. Cole, M. C. Payne, and C.-K. Skylaris. Submitted (2011) .
• Large-scale DFT calculations in implicit solvent { a case study on the T4 lysozyme L99A/M102Q protein. J. Dziedzic, S. J. Fox, T. Fox, C. S. Tautermann, and C.-K. Skylaris. Submitted (2011) .

Articles

• Theoretical Science feature article about projects (including ONETEP) carried out with contributions from Cambridge University's Physics-Chemistry EPSRC portfolio partnership funding. EPSRC Newsline, issue 30, Summer2004.
• Final report of workshop on "Linear-scaling ab initio calculations: applications and future directions" which was held at CECAM, Lyon, France between 3 and 6 September 2007.