Generation of Quantum Configurational Ensembles Using Approximate Potentials. J.Morado, P.N. Mortens, J.W.M. Nissink, M.L. Verdonk, R.A. Ward, J. W. Essex, C.-K. Skylaris, J. Chem. Theory Comput. 2021, 17, 11, 7021–7042 (pdf)
Materials and Molecular Modelling at the Exascale. T. Keal, A.-M. Elena, K. Stoneham, M. Probert, C. Cucinotta, A. Logsdail, A.Zen, P. Hasnip, I. Bush, M. Watkins, D. Alfe, C.-K. Skylaris, B. Curchod, Q. Cai, S. Woodley Computing in Science & Engineering vol. 24, no. 01, pp. 36-45, 2022 (pdf)
Massively parallel linear-scaling Hartree-Fock exchange and Hybrid exchange-correlation functionals with plane wave basis set accuracy. J.Dziedzic, J.C. Womack, R.Ali, and C.-K. Skylaris. J.Chem.Phys. 155, 224106 (2021)(pdf)
Electrochemistry from first-principles in the grand canonical ensemble. A. Bhandari, C. Peng, J. Dziedzic, L. Anton, J. R. Owen, D. Kramer, and C.-K. Skylaris. J. Chem. Phys 155 (2021) 024114 (pdf)
ParaMol: A Package for Automatic Parameterization of Molecular Mechanics Force Fields. J. Morado, P. N. Mortenson, M. L. Verdonk, R. A. Ward, J. W. Essex, and C.-K. Skylaris. J. Chem. Inf. Model. 61 (2021) 2026-2047 (pdf)
Challenges for large scale simulation: general discussion. J. G. Brandenburg, K. Burke, B. Civalleri, D. J. Cole, G. Csányi, G. David, N. I. Gidopoulos, D. Gowland, T. Helgaker, M. F. Herbst, B. Hourahine, T. J. P. Irons, C. R. Jacob, P.-F. Loos, N. Mehta, M. R. Mulay, J. Neugebauer, K. Pernal, A. Pribram-Jones, P. Romaniello, M. R. Ryder, A. Savin, D. Sirbu, C.-K. Skylaris, D. G. Truhlar, J. Wetherell, and W. Yang. Faraday Discuss. 224 (2020) 309-332 (pdf)
New density-functional approximations and beyond: general discussion. J. G. Brandenburg, K. Burke, A. Cancio, J. Erhard, E. Fromager, A. Ghosal, N. Gidopoulos, P.Gori-Giorgi, T. Helgaker, B. Hourahine, C. R. Jacob, D. Kooi, N. Maitra, M. R. Mulay, K. Pernal, A. Pribram-Jones, L. Reining, P. Romaniello, M. R. Ryder, A. Savin, C.-K. Skylaris, A. M. Teale, D. Tozer, D. G. Truhlar, and W. Yang. Faraday Discuss. 224 (2020) 166-200 (pdf)
Electronic structure calculations in electrolyte solutions: Methods for neutralization of extended charged interfaces. A. Bhandari, L. Anton, J. Dziedzic, C. Peng, D. Kramer, and C.-K. Skylaris. J. Chem. Phys. 153 (2020) 124101 (pdf)
The ONETEP linear-scaling density functional theory program. J. C. A. Prentice, J. Aarons, J. C. Womack, A. E. A. Allen, L. Andrinopoulos, L. Anton, R. A. Bell, A. Bhandari, G. A. Bramley, R. J. Charlton, R. J. Clements, D. J. Cole, G. Constantinescu, F. Corsetti, S. M.-M. Dubois, K. K. B. Duff, J. M. Escartín, A. Greco, Q. Hill, L. P. Lee, E. Linscott, D. D. O’Regan, M. J. S. Phipps, L. E. Ratcliff, Á. R. Serrano, E. W. Tait, G. Teobaldi, V. Vitale, N. Yeung, T. J. Zuehlsdorff, J. Dziedzic, P. D. Haynes, N. D. M. Hine, A. A. Mostofi, M. C. Payne, and C.-K. Skylaris. J. Chem. Phys. 152 (2020) 174111 (pdf)
Electron localisation descriptors in ONETEP: a tool for interpreting localisation and bonding in large-scale DFT calculations. R. J. Clements, J. C. Womack, and C.-K. Skylaris. Electron. Struct. 2 (2020) 027001 (pdf)
Practical Approach to Large-Scale Electronic Structure Calculations in Electrolyte Solutions via Continuum-Embedded Linear-Scaling Density Functional Theory. J. Dziedzic, A. Bhandari, L. Anton, C. Peng, J. C. Womack, M. Famili, D. Kramer, and C.-K. Skylaris. J. Phys. Chem. C. 124 (2020) 7860-7872 (pdf)
Atom-projected and angular momentum resolved density of states in the ONETEP code. J. Aarons, L. G. Verga, N. D. M. Hine, and C.-K. Skylaris. Electron. Struct. 1 (2019) 035002 (pdf)
Mutually Polarizable QM/MM Model with in situ Optimized Localized Basis Functions. J. Dziedzic, T. Head-Gordon, M. Head-Gordon, and C.-K. Skylaris. J. Chem. Phys. 150 (2019) 074103 (pdf)
Surface Reconstruction Amendment to the Intrinsic Sampling Method. F. G. J. Longford, J. W. Essex, C.-K. Skylaris, and J. G. Frey. J. Chem. Phys. 149 (2018) 234705 (pdf)
Unexpected Finite Size Effects in Interfacial Systems: Why Bigger is not Always Better—Increase in Uncertainty of Surface Tension with Bulk Phase Width. F. G. J. Longford, J. W. Essex, C.-K. Skylaris, and J. G. Frey. J. Chem. Phys. 148 (2018) 214704 (pdf)
DL_MG: A Parallel Multigrid Poisson and Poisson-Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution. J. C. Womack, L. Anton, J. Dziedzic, P. Hasnip, M. Probert, and C.-K. Skylaris. J. Chem. Theor. Comput. 14 (2018) 1412-1432 (pdf)
Electronic Annealing Fermi Operator Expansion for DFT Calculations on Metallic Systems. J. Aarons, and C.-K. Skylaris. J. Chem. Phys. 148 (2018) 074107 (pdf)
Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis. Y. Mao, Y. Shao, J. Dziedzic, C. -K. Skylaris, T. Head-Gordon, and M. Head-Gordon. J. Chem. Theory Comput. 13 (2017) 1963-1979 (pdf)
A Monte Carlo Resampling Approach for the Calculation of Hybrid Classical and Quantum Free Energies. C. Cave-Ayland, C.-K. Skylaris, and J.W. Essex. J. Chem. Theory Comput. 13 (2017) 415-424 (pdf)
Perspective: Methods for Large-Scale Density Functional Calculations on Metallic Systems. J. Aarons, M. Sarwar, D. Thompsett, and C.-K. Skylaris. J. Chem. Phys. 145 (2016) 220901 (pdf)
Use of the rVV10 Nonlocal Correlation Functional in the B97M-V Density Functional: Defining B97M-rV and Related Functionals. N. Mardirossian, L. R. Pestana, J. C. Womack, C.-K. Skylaris, T. Head-Gordon, and M. Head-Gordon. J. Phys. Chem. Lett. 8 (2016) 35-40 (pdf)
Self-consistent Implementation of Meta-GGA Functionals for the ONETEP Linear-Scaling Electronic Structure Package. J.C. Womack, N. Mardirossian, M. Head-Gordon, and C.-K. Skylaris. J. Chem. Phys. 145 (2016) 204114 (pdf)
TINKTEP: A fully self-consistent, mutually-polarizable QM/MM approach based on the AMOEBA force field. J. Dziedzic, Y. Mao, Y. Shao, J. Ponder, T. Head-Gordon, M. Head-Gordon, and C.-K. Skylaris. J. Chem. Phys. 145 (2016) 124106 (pdf)
Advanced Potential Energy Surfaces for Molecular Simulation. A. Albaugh, H. A. Boateng, R. T. Bradshaw, O. N. Demerdash, J. Dziedzic, Y. Mao, D. T. Margul, J. M. Swails, Q. Zeng, D. A. Case, P. K. Eastman, J. W. Essex, M. Head-Gordon, V. S. Pande, J. W. Ponder, Y. Shao, C.-K. Skylaris, I. T. Todorov, M. E. Tuckerman, and T. Head-Gordon. J. Phys. Chem. B 120 (2016) 9811-9832 (pdf)
Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation. Y. Mao, P. R. Horn, N. Mardirossian, T. Head-Gordon, C.-K. Skylaris, and M. Head-Gordon. J. Chem. Phys. 145 (2016) 044109 (pdf)
Energy decomposition analysis based on absolutely localised molecular orbitals for large-scale density functional theory calculations in drug design. M. J. S. Phipps, T. Fox, C. S. Tautermann, and C.-K. Skylaris. J. Chem. Theory Comput. 12 (2016) 3135-3148 (pdf)
A benchmark for materials simulation. C.-K. Skylaris. Science. 351 (2016) 1394-1395 (pdf)
What Is the Price of Open-Source Software? A. I. Krylov, J. M. Herbert, F. Furche, M. Head-Gordon, P. J. Knowles, R. Lindh, F. R. Manby, P. Pulay, C.-K. Skylaris, and H.-J. Werner Chem. Phys. Lett. 6 (2015) 2751-2754 (pdf)
Anharmonic Infrared Spectroscopy through the Fourier Transform of Time Correlation Function Formalism in ONETEP. V. Vitale, J. Dziedzic, S. M.-M. Dubois, H. Fangohr, and C.-K. Skylaris. J. Chem. Theory Comput. 11 (2015) 3321-3332 (pdf)
A "Stepping Stone" Approach for Obtaining Quantum Free Energies of Binding. C. Sampson, T. Fox, C. S. Tautermann, C. J. Woods, and C.-K. Skylaris. J. Phys. Chem. B 119 (2015) 7030-7040 (pdf)
Optimised three-dimensional Fourier interpolation: An analysis of techniques and application to a linear-scaling density functional theory code. F. P. Russell, K. A. Wilkinson, P. H. J. Kelly, and C.-K. Skylaris. Comput. Phys. Commun. 187 (2015) 8-19 (pdf)
Hybrid MPI-OpenMP Parallelism in the ONETEP Linear-Scaling Electronic Structure Code: Application to the Delamination of Cellulose Nanofibrils. K. A. Wilkinson, N. D. M. Hine, and C.-K. Skylaris. J. Chem. Theory Comput. 10 (2014) 4782-4794 (pdf)
Expanding the Scope of Density Derived Electrostatic and Chemical Charge Partitioning to Thousands of Atoms. L. P Lee, N. G. Limas, D. J. Cole, M. C. Payne, C.-K. Skylaris, and T. A. Manz. J. Chem. Theory Comput. 10 (2014) 5377-5390 (pdf)
The application of molecular dynamics to fitting EXAFS data. S. W. T. Price, N. Zonias, C.-K. Skylaris, A. E. Russell, and B. Ravel. J. Chem. Phys. 430 (2013) 012009 (pdf)
Variationally-localized search direction method for constrained optimization of non-orthogonal, localized orbitals in electronic structure calculations. A. Ruiz-Serrano, and C.-K. Skylaris. J. Chem. Phys. 139 (2013) 164110 (pdf)
Linear-scaling calculation of Hartree-Fock exchange energy with Non-orthogonal Generalised Wannier Functions. J. Dziedzic, Q. O. Hill, and C.-K. Skylaris. J. Chem. Phys. 139 (2013) 214103 (pdf)
Porting ONETEP to Graphical Processing Unit based Coprocessors: 1. FFT box Operations. K. Wilkinson, and C.-K. Skylaris. J. Comput. Chem. 34 (2013) 2446-2459 (pdf)
A variational method for density functional theory calculations on metallic systems with thousands of atoms. A. Ruiz-Serrano, and C.-K. Skylaris. J. Chem. Phys. 139 (2013) 054107 (pdf)
Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning. L. P. Lee, D. J. Cole, C. -K. Skylaris, W. L. Jorgensen, and M. C. Payne. J. Chem. Theory Comput. 9 (2013) 2981-2991 (pdf)
Natural Bond Orbital Analysis in the ONETEP Code: Application to Large Protein Systems. L. P. Lee, D. J. Cole, M. C. Payne, and C.-K. Skylaris. J. Comput. Chem. 34 (2013) 429-444 (pdf)
Pulay forces from localized orbitals optimized in situ using a psinc basis set. A. Ruiz-Serrano, N. D. M. Hine, and C.-K. Skylaris, J. Chem. Phys. 136 (2012) 234101 (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)
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)
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)
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)
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)
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) 1041-1053 (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) 669-683 (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)
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) 345-349 (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) 143-148 (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 (2006) 2489-2499 (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 (2006) 973-988 (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) 3485-3492 (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)
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 (2003) 8842-8848 (pdf)
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) 788-802 (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)
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 (2001) 315-322 (pdf)
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. 19 (2000) 327-362 (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) 445-451 (pdf)
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) 187-193 (pdf)
Papers in Journals - Applications
Calculating shear viscosity with confined non-equilibrium molecular dynamics: a case study on hematite – PAO-2 lubricant. D.Mathas, D. Sarpa, W. Holweger, M.Wolf, C.Bohnert, V. Bakolas, J. Procelewska, J. Franke, P. Rödel, C.-K. Skylaris. RSC Adv., 2023, 13, 33994-34002 (pdf)
A Workflow for Identifying Viable Crystal Structures with Partially Occupied Sites Applied to the Solid Electrolyte Cubic Li7La3Zr2O12. J. Holland, T. Demeyere, A. Bhandari, F. Hanke, V. Milman, C.-K. Skylaris J. Phys. Chem. Lett. 2023, 14, XXX, 10257–10262 (pdf)
Linear-scaling density functional theory (DFT) simulations of point, Frenkel and Schottky defects in CeO2. N.Anwar, R. M. Harker, M. T. Storr, M. Molinari, C.-K. Skylaris. Computational Materials Science 229 (2023) (pdf)
Does a Machine-Learned Potential Perform Better Than An Optimally Tuned Traditional Force Field? A Case Study on Fluorohydrins. J. Morado, P.N. Mortenson, J.W.M. Nissink, J.W. Essex, C.-K. Skylaris. . J. Chem. Inf. Model. 2023 (pdf)
Computing Viscosities of Mixtures of Ester-Based Lubricants at Different Temperatures. D. Sarpa, D. Mathas, V. Bakolas, J. Proceleewska, J. Franke, M. Busch, P. Roedel, C. Bohnert, M. Wolf, C.-K. Skylaris J. Phys. Chem. B 2023, 127, 11, 2587–2594 (pdf)
Atomistic simulations on the carbidisation processes in Pd nanoparticles. A. Kordatos, K. Mohammed, R. Vakili, A. Goguet, H.Manyer, E.Gibson, M.Carravetta, P. Wells, C.-K.Skylaris RSC Adv., 2023, 13, 5619-5626 (pdf)
Using molecular dynamics to simulate realistic structures of nitrocellulose of different nitration levels. C. Gibbon, P. Di Pietro, M. Storr, D. Broughton, C.-K. Skylaris Phys. Chem. Chem. Phys., 2023, (pdf)
BRD4: Quantum mechanical protein-ligand binding free energies using the full protein DFT-based QM-PBSA method. L. Gundelach, T. Fox, C. S. Tautermann, C.-K. Skylaris, Phys. Chem. Chem. Phys., 2022,24, 25240-25249 (pdf)
Ab initio study of lithium intercalation into a graphite nanoparticle. J. Holland, A. Bhandari, D. Kramer, V. Milman, F. Hanke, C.-K. Skylaris, Materials Advances, 2022, 3, 8469 - 8484 (pdf)
Li nucleation on the graphite anode under potential control in Li-ion batteries. A. Bhandari, C. Peng, J. Dziedzic, J.R. Owen, D. Kramer, C.-K. Skylaris, J. Mater. Chem. A, 2022,10, 11426-11436 (pdf)
Understanding Adsorption of Organic on Pt(111) in Aqueous Phase:Insights from DFT Based Implicit Solvent and Statistical Thermodynamics Models. G.A.Bramley, M.-T. Nguyen, V.-A. Glezakou, R.Rousseau, C.-K. Skylaris. J. Chem. Theory Comput. 2022, 18, 3, 1849–1861 (pdf)
Atomistic level characterisation of ssDNA translocation through the E.coli proteins CsgG and CsgF for nanopore sequencing. P.Rattu, F. Glencross, S. L.Mader, C.-K. Skylaris, S. J. Matthews, S.L. Rouse, S. Khalid Computational and Structural Biotechnology Journal, 19 (2021), 6417-6430 (pdf)
Pushing the boundaries of lithium battery research with atomistic modelling on different scales. L. M. Morgan, M. Mercer, A. Bhandari, C. Peng, M. M. Islam, H. Yang, J. O. Holland, S. W. Coles, R. Sharpe, A. Walsh, B. J. Morgan, D. Kramer, S. M. Islam, H. Hoster, J. S. Edge, C.-K. Skylaris. Prog. Energy 4 (2022) 012002(pdf)
Mechanism of Li nucleation at graphite anodes and mitigation strategies. C. Peng, A. Bhandari, J. Dziedzic, J. R. Owen, C.-K. Skylaris, and D. Kramer. J. Mater. Chem. A, 2021,9, 16798-16804 (pdf)
Evaluation of methods for viscosity simulations of lubricants at different temperatures and pressures: a case study on PAO-2. D. Mathas, W. Holweger, M. Wolf, C. Bohnert, V. Bakolas, J. Procelewska, L. Wang, S. Bair, and C.-K. Skylaris. Tribol. Trans. 64 (2021) 1138–1148 (pdf)
Intercalation voltages for spinel LixMn2O4 (0≤x≤2) cathode materials: Calibration of calculations with the ONETEP linear-scaling DFT code. R. Ledwaba, J. C. Womack, C.-K. Skylaris, and P. E. Ngoepe. Mater. Today Commun. 27 (2021) 102380 (pdf)
Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional. L. Gundelach, T. Fox, C. S. Tautermann, and C.-K. Skylaris. Phys. Chem. Chem. Phys. 23 (2021) 9381–9393 (pdf)
Analysis of DNA Interactions and GC Content with Energy Decomposition in Large-Scale Quantum Mechanical Calculation. H. Chen, and C.-K. Skylaris. Phys. Chem. Chem. Phys. 23 (2021) 8891-8899 (pdf)
Translocation of flexible and tensioned ssDNA through in silico designed hydrophobic nanopores with two constrictions. P. Rattu, B. Belzunces, T. Haynes, C.-K. Skylaris, and S. Khalid. Nanoscale 13 (2021) 1673-1679 (pdf)
Strain effects in core-shell PtCo nanoparticles: a comparison of experimental observations and computational modelling. T. Ellaby, A. Varambhia, X. Luo, L. Briquet, M. Sarwar, D. Ozkaya, D. Thompsett, P. D. Nellist, and C.-K. Skylaris. Phys. Chem. Chem. Phys. 22 (2020) 24784-24795 (pdf)
Lithium intercalation edge effects and doping implications for graphite anodes. C. Peng, M. P. Mercer, C.-K. Skylaris, and D. Kramer. J. Mater. Chem. A. 8 (2020) 7947–7955 (pdf)
The role of electrostatics in enzymes: do biomolecular force fields reflect protein electric fields? R. T. Bradshaw, J. Dziedzic, C.-K. Skylaris, and J. W. Essex. J. Chem. Inf. Model. 60 (2020) 3131-3144 (pdf)
Reconciling Work Functions and Adsorption Enthalpies for Implicit Solvent Models: A Pt (111)/Water Interface Case Study. G. Bramley, M.-T. Nguyen, V.-A. Glezakou, R. Rousseau, and C.-K. Skylaris. J. Chem. Theor. Comput. 16 (2020) 2703–2715 (pdf)
Meta-analysis: the molecular organization of non-fullerene acceptors. P. Mondelli, G. Boschetto, P. Horton, P. Tiwana, C.-K. Skylaris, S. Coles, M. Krompiec, and G. Morse. Mater. Horiz. 7 (2020) 1062-1072 (pdf)
Mechanism of the Os-Catalyzed Oxidative Cyclization of 1,5-Dienes. A. Husseiin, M. Phipps, C.-K. Skylaris, and R. Brown. J. Org. Chem. 84 (2019) 15173−15183 (pdf)
How Does Polymorphism Affect the Interfacial Charge-Transfer States in Organic Photovoltaics? G. Boschetto, M. Krompiec, and C.-K. Skylaris. J. Phys. Chem. C. 123 (2019) 25585-25595 (pdf)
Modification of O and CO binding on Pt nanoparticles due to electronic and structural effects of titania supports. T. Ellaby, L. Briquet, M. Sarwar, D. Thompsett, and C.-K. Skylaris. J. Chem. Phys. 151 (2019) 114702 (pdf)
Machine-Learned Fragment-Based Energies for Crystal Structure Prediction. D. McDonagh, C.-K. Skylaris, and G. M. Day. J. Chem. Theory Comput. 15 (2019) 2743-2758 (pdf)
Ethanol, O, and CO Adsorption on Pt Nanoparticles: Effects of Nanoparticle Size and Graphene Support. L. G. Verga, A. E. Russell, and C.-K. Skylaris. Phys. Chem. Chem. Phys. 20 (2018) 25918 (pdf)
Surfactant Proteins A and D – Trimerized Innate Immunity Proteins with an Affinity for Viral Fusion Proteins. A. Watson, M. Phipps, H. Clark, C.-K. Skylaris, and J. Madsen. J. Innate Immun. 11 (2018) 13-28 (pdf)
Insights into the Charge-Transfer Mechanism of Organic Photovoltaics: Effect of Domain Size. G. Boschetto, M. Krompiec, and C.-K. Skylaris. J. Phys. Chem. C. 122 (2018) 17024–17034 (pdf)
Molecular Dynamics Simulation of Potentiometric Sensor Response: Effect of Biomolecules, Surface Morphology and Surface Charge. B. M. Lowe, C.-K. Skylaris, N. G. Green, Y. Shibuta, and T. Sakata. Nanoscale 10 (2018) 8650-8666 (pdf)
Calculation of Surface Potentials at the Silica–Water Interface Using Molecular Dynamics: Challenges and Opportunities. B. M. Lowe, C.-K. Skylaris, N. G. Green, Y. Shibuta, and T. Sakata. Jpn. J. Appl. Phys. 57 (2018) 04FM02 (pdf)
Ideal vs Real: Simulated Annealing of Experimentally Derived and Geometric Platinum Nanoparticles. T. H. Ellaby, J. Aarons, A. Varambhia, L. Jones, P. Nellist, D. Özkaya, M. Sarwar, D. Thompsett, and C.-K. Skylaris. J. Phys. Condens. Matter. 30 (2018) 155301 (pdf)
DFT Calculation of Oxygen Adsorption on Platinum Nanoparticles: Coverage and Size Effects. L. G. Verga, J. Aarons, M. Sarwar, D. Thompsett, A. E. Russell, and C.-K. Skylaris. Faraday Discuss. 208 (2018) 497-522 (pdf)
CD1b-Restricted GEM T Cell Responses are Modulated by Mycobacterium Tuberculosis Mycolic Acid Meromycolate Chains. A. Chancellor, A. S. Tocheva, C. Cave-Ayland, L. Tezera, A. White, J. R. Al Dulayymi, J. S. Bridgeman, I. Tews, S. Wilson, N. M. Lissin, M. Tebruegge, B. Marshall, S. Sharpe, T. Elliott, C.-K. Skylaris, J. W. Essex, M. S. Baird, S. Gadola, P. Elkington, and S. Mansour. Proc. Natl. Acad. Sci. USA 51 (2017) E10956-E10964 (pdf)
Field-Effect Sensors – From pH sensing to Biosensing: Sensitivity Enhancement using Streptavidin-Biotin as a Model System. B. M. Lowe, K. Sun, I. Zeimpekis, C. -K. Skylaris, and N. G. Green. Analyst 142 (2017) 4173-4200 (pdf)
Electronically Excited States in Solution via a Smooth Dielectric Model Combined with Equation-of-Motion Coupled Cluster Theory. J. Coleman Howard, J. C. Womack, J. Dziedzic, C. -K. Skylaris, B. P. Pritchard, and T. D. Crawford. J. Chem. Theory Comput. 13 (2017) 5572-5581 (pdf)
Predicting the Oxygen-Binding Properties of Platinum Nanoparticle Ensembles by Combining High-Precision Electron Microscopy and Density Functional Theory. J. Aarons, L. Jones, A. Varambhia, K. E. MacArthur, D. Ozkaya, M. Sarwar, C.-K. Skylaris, and P. D. Nellist. Nano Lett. 17 (2017) 4003-4012 (pdf)
Performance of Extended Lagrangian Schemes for Molecular Dynamics Simulations with Classical Polarizable Force Fields and Density Functional Theory. V. Vitale, J. Dziedzic, A. Albaugh, A.M.N. Niklasson, T. Head-Gordon and C.-K. Skylaris. J. Chem. Phys. 146 (2017) 124115 (pdf)
Intuitive Density Functional Theory-Based Energy Decomposition Analysis for Protein-Ligand Interactions. M.J.S. Phipps, T. Fox, C.S. Tautermann, and C.-K. Skylaris. J. Chem. Theory Comput. 13 (2017) 1837-1850 (pdf)
Linear-scaling Density Functional Simulations of the Effect of Crystallographic Structure on the Electronic and Optical Properties of Fullerene Solvates. H. Xue, G. Boschetto, M. Krompiec, G.E. Morse, F. Tang, and C.-K. Skylaris. Phys. Chem. Chem. Phys. 19 (2017) 5617-5628 (pdf)
Effect of Polymerization Statistics on the Electronic Properties of Copolymers for Organic Photovoltaics. G. Boschetto, H. Xue, J. Dziedzic, M. Krompiec, and C.-K. Skylaris. J. Phys. Chem. C. 121 (2017) 2529-2538 (pdf)
Dynamic Behaviour of the Silica-Water-Bio Electrical Double Layer in the Presence of a Divalent Electrolyte. B. M. Lowe, Y. Maekawa, Y. Shibuta, T. Sakata, C.-K. Skylaris, and N. G. Green. Phys. Chem. Chem. Phys. 19 (2017) 2687-2701 (pdf)
Effect of Graphene Support on Large Pt Nanoparticles. L. G. Verga, J. Aarons, M. Sarwar, D. Thompsett, A. E. Russell, and C.-K. Skylaris. Phys. Chem. Chem. Phys. 18 (2016) 32713 (pdf)
Chemically Selective Alternatives to Photoferroelectrics for Polarization-Enhanced Photocatalysis: The Untapped Potential of Hybrid Inorganic Nanotubes. J. D. Elliott, E. Poli, I. Scivetti, L. E. Ratcliff, L. Andrinopoulos, J. Dziedzic, N. D. M. Hine, A. A. Mostofi, C.-K. Skylaris, P. D. Haynes, and G. Teobaldi. Adv. Sci. (2016) 1600153 (pdf)
Cholesteryl esters stabilize human CD1c conformations for recognition by self-reactive T cells. S. Mansour, A. S. Tocheva, C. Cave-Ayland, M. M. Machelett, B. Sander, N. M. Lissin, P. E. Molloy, M. S. Baird, G. Stübs, N. W. J. Schröder, R. R. Schumann, J. Rademann, A. D. Postle, B. K. Jakobsen, B. G. Marshall, R. Gosain, P. T. Elkington, T. Elliott, C.-K. Skylaris, J. W. Essex, I. Tews, and S. D. Gadola. PNAS. 113 (2016) E1266-E1275 (pdf)
The potential of imogolite nanotubes as (co-)photocatalyst: a linear-scaling density functional theory study. E. Poli, J. Elliott, L. Ratcliff, L. Andrinopoulos, J. Dziedzic, N. Hine, A. Mostofi, C.-K. Skylaris, P. Haynes, and G. Teobaldi. J. Phys. Condens. Matter. 28 (2015) 074003 (pdf)
Spectroscopic chemical insights leading to the design of versatile sustainable composites for enhanced marine application. A. S. Dzielendziak, J. I. R. Blake, R. Bounds, K. A. Wilkinson, M. Carravetta, A R. Chambers, C.-K. Skylaris, and R. Raja. R. Soc. Chem. Adv. 5 (2015) 101221 (pdf)
Energy decomposition analysis approaches and their evaluation on prototypical protein–drug interaction patterns. M. J. S. Phipps, T. Fox, C. S. Tautermann, and C.-K. Skylaris. Chem. Soc. Rev. 44 (2015) 3177-3211 (pdf)
Acid-Base Dissociation Mechanisms and Energetics at the Silica-Water Interface: An Activationless Process, B. M. Lowe, C.-K. Skylaris, and N. G. Green. J. Colloid Interface Sci. 451 (2015) 231-244 (pdf)
A computational study of vicinal fluorination in 2,3-difluorobutane: implications for conformational control in alkane chains. S. J. Fox, S. Gourdain, A. Coulthurst, C. Fox, I. Kuprov, J. W. Essex, C.-K. Skylaris, and B. Linclau. Chem. Eur. Jour. 21 (2015) 1682-1691 (pdf)
Direct Validation of the Single Step Classical to Quantum Free Energy Perturbation. C. Cave-Ayland, C.-K. Skylaris, and J. W. Essex. J. Phys. Chem. B 119 (2015) 1017-1025 (pdf)
Large-Scale Density Functional Theory Transition State Searching in Enzymes. G. Lever, D. J. Cole, R. Lonsdale, K. E. Ranaghan, D. J. Wales, A. J. Mulholland, C. -K. Skylaris, and M. C. Payne. J. Phys. Chem. Lett. 5 (2014) 3614-3619 (pdf)
Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site. S. J. Fox, J. Dziedzic, T. Fox, C. S. Tautermann, and C.-K. Skylaris. Proteins 82 (2014) 3335-3346 (pdf)
Free Energies of Binding from Large-Scale First Principles Quantum Mechanical Calculations: Application to Ligand Hydration Energies. S.J. Fox, C. Pittock, C.S. Tautermann, T. Fox, C. Christ, N.O.J. Malcolm, J.W. Essex, and C.-K. Skylaris. J. Phys. Chem. B 117 (2013) 9478-9485 (pdf)
A predictive science approach to aid understanding of electrospray ionisation tandem mass spectrometric fragmentation pathways of small molecules using density functional calculations. A. Galezowska, M. W. Harrison, J. M. Herniman, C.-K. Skylaris, and G. John Langley. Rapid. Commun. Spectrom. 27 (2013) 964-970 (pdf)
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. Int. J. Quant. Chem. 113 (2013) 771-785 (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. Phys. Rev. B 85 (2012) 075439 (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)
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) 1102-1108 (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)
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)
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) 749-759 (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)
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)
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) 5141-5153 (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) 5757-5769 (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) 4593-4600 (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) 355-363 (pdf)
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)
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) 3111-3114 (pdf)
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) 229-239 (pdf)
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) 47-55 (pdf)
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 (1999) 1831-1837 (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) 11727-11731 (pdf)
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) 1701-1706 (pdf)
Articles
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.
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, Summer 2004.