Prof Chris Skylaris 
Professor of Computational Chemistry, University of Southampton


Chris’s research focuses on the development of theory, algorithms and codes for quantum mechanical (QM) calculations from first principles on parallel computers. He is a founding and leading author of the ONETEP program for large-scale (linear-scaling) quantum chemistry simulations. While his developments are based on fundamental science, they are often motivated by the need to provide solutions to challenging chemistry problems such as new materials, catalysis and drug design. Many of these problems require simulations of many orders of magnitude in time- and length-scales so another focus of his research is to develop multiscale simulation approaches where the quantum simulations which cover the microscopic electronic and atomistic scale are coupled with simulation methods suitable for larger scales. He is a committee member of the CCP9 group, and the UK Car-Parrinello Consortium. He is the author of over 190 publications in international peer-reviewed journals. His research has been supported by RCUK (EPSRC, BBSRC, MRC), the Faraday Institution, the Royal Society, NSF, CNPq, as well as industry with collaborative projects with Boehringer Ingelheim, BIOVIA, AWE, Schaeffler, Johnson Matthey, Astex, AZ, and Merck.


Abstract: Large-scale quantum atomistic biomolecular simulations

First-principles quantum-mechanical simulations, based on density-functional theory (DFT), are today used hand in hand with experimental methods for synthesis and characterization of new materials. Conventional DFT has a computational effort which scales with the third power in the number of atoms and this limits the practical size of calculations. ONETEP [1] is a world-leading UK-developed software package (free to academics) which uses a linear-scaling DFT framework to enable calculations on much larger sizes (many thousands of atoms), offering unmatched capabilities for simulating more realistic models of materials and their environment in multiscale simulations. With ONETEP we can for the first time treat fully quantum mechanically interactions between entire biomolecular assemblies such as protein-protein, DNA, and protein-ligand. These simulations avoid the empiricism of heavily parametrized biomolecular simulation methods such as force fields and explicitly account for all the physical interactions. They provide much “added value” because apart from energetic and structural information they also produce a host of electronic properties such as an accurate representation of the whole electronic density, molecular orbitals, and charges on atoms. In this talk I will summarise applications of ONETEP to biomolecular problems such as protein-ligand binding [2,3] and enzyme catalysis [4,5].

 

[1] 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.

[2] 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.24 (2022) 25240.

[3] 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.

[4] 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

[5] 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.

 


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