arXiv subjects

Chris-Kriton Skylaris

Publications and source records attributed to Chris-Kriton Skylaris.

7 recordsLinked to original sources

arXiv2026

Scientific applications of quantum computing: challenges and opportunities

The predictive simulation of molecules and materials has had a broad and significant impact. It nevertheless remains constrained by the cost of accurately treating electronic correlation, excited states, and complex energy landscapes. Quantum computing offers a fundamentally different computational paradigm in which quantum states are encoded and manipulated directly rather than approximated on classical hardware. Here we discuss where this approach may provide a genuine scientific advantage in chemistry, materials science, and biochemistry. Promising directions include the high-accuracy treatment of correlated active spaces, improved excited-state simulations, and accelerated exploration of combinatorial structure spaces. The central challenge is therefore not qubit scaling alone, but demonstrably chemically meaningful gains in predictive reliability. We argue that near-term value is most likely to come from disciplined workflow integration rather than wholesale replacement of classical methods. Noisy physical devices, error-mitigated utility experiments, early fault-tolerant devices, and fully fault-tolerant quantum computers offer different scientific prospects, and claims of usefulness must be tied to the specific regime being discussed. Quantum computing will become scientifically valuable when it demonstrably reduces uncertainty in computed energies, rates, spectra, or materials stability after the full costs of state preparation, measurement, error handling, and coupling to classical simulation are included.

quant-ph↗

arXiv2025

Spin-Dependent Nonorthogonal Generalized Wannier Functions and their Integration with PAW and Hubbard Corrections in Linear-Scaling DFT

We present a spin-dependent extension of the non-orthogonal generalized Wannier function (NGWF) formalism within the framework of linear-scaling density functional theory (LS-DFT) as implemented in the ONETEP code. In traditional LS-DFT representations, both spin channels are constrained to share a common variational basis, which limits the accuracy for systems that are spin-polarized or exhibit magnetic order. Our approach allows NGWFs to vary independently for each spin channel, enabling a more accurate representation of spin-polarization in the electronic density. We demonstrate the efficacy of this method through a series of test cases, including localized magnetic defects in two-dimensional hBN, transition metal complexes, two-dimensional van der Waals magnetic materials, and both bulk and nanocluster ferromagnetic Co. In each scenario, the incorporation of spin-dependent NGWFs results in enhanced accuracy for total energy calculations, improved localization of spin density, and accurate predictions of magnetic ground states. This improvement is particularly notable when combined with DFT+U and DFT+U+J corrections. In this work, we take the opportunity to describe the combination of DFT+U+J and the projector-augmented wave (PAW) formalism within the LS-DFT framework, including how PAW participates in the ionic Pulay force, and in the minimum-tracking linear response approach for computing parameters in situ. Our findings demonstrate that spin-dependent NGWFs are a crucial and computationally efficient advancement in the linear-scaling DFT simulation of spin-polarized materials.

cond-mat.mtrl-sci↗

arXiv2011

Minimal parameter implicit solvent model for ab initio electronic structure calculations

We present an implicit solvent model for ab initio electronic structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comp. Chem. 23, 6 (2002)). While this model depends on only two parameters, we demonstrate that by using appropriate boundary conditions and dispersion-repulsion contributions, solvation energies obtained for an extensive test set including neutral and charged molecules show dramatic improvement compared to existing models. Our approach is implemented in, but not restricted to, a linear-scaling density functional theory (DFT) framework, opening the path for self-consistent implicit solvent DFT calculations on systems of unprecedented size, which we demonstrate with calculations on a 2615-atom protein-ligand complex.

physics.comp-ph↗

arXiv2008

Novel structural features of CDK inhibition revealed by an ab initio computational method combined with dynamic simulations

The rational development of specific inhibitors for the ~500 protein kinases encoded in the human genome is impeded by a poor understanding of the structural basis for the activity and selectivity of small molecules that compete for ATP binding. Combining classical dynamic simulations with a novel ab initio computational approach linear-scalable to molecular interactions involving thousands of atoms, we have investigated the binding of five distinct inhibitors to the cyclin-dependent kinase CDK2. We report here that polarization and dynamic hydrogen bonding effects, so far undetected by crystallography, affect both their activity and selectivity. The effects arise from the specific solvation patterns of water molecules in the ATP binding pocket or the intermittent formation of hydrogen bonds during the dynamics of CDK/inhibitor interactions and explain the unexpectedly high potency of certain inhibitors such as 3-(3H-imidazol-4-ylmethylene)-5-methoxy-1,3-dihydro-indol-2-one (SU9516). The Lys89 residue in the ATP-binding pocket of CDK2 is observed to form temporary hydrogen bonds with the three most potent inhibitors. This residue is replaced in CDK4 by Thr89, whose shorter side-chain cannot form similar bonds, explaining the relative selectivity of the inhibitors for CDK2. Our results provide a generally applicable computational method for the analysis of biomolecular structures and reveal hitherto unrecognized features of the interaction between protein kinases and their inhibitors

physics.bio-ph↗

arXiv2005

Using ONETEP for accurate and efficient O(N) density functional calculations

We present a detailed comparison between ONETEP, our linear-scaling density functional method, and the conventional pseudopotential plane wave approach in order to demonstrate its high accuracy. Further comparison with all-electron calculations shows that only the largest available Gaussian basis sets can match the accuracy of routine ONETEP calculations. Results indicate that our minimisation procedure is not ill-conditioned and that convergence to self-consistency is achieved efficiently. Finally we present calculations with ONETEP, on systems of about 1000 atoms, of electronic, structural and chemical properties of a wide variety of materials such as metallic and semiconducting carbon nanotubes, crystalline silicon and a protein complex.

cond-mat.mtrl-sci↗

arXiv2001

Comparison of variational real-space representations of the kinetic energy operator

We present a comparison of real-space methods based on regular grids for electronic structure calculations that are designed to have basis set variational properties, using as a reference the conventional method of finite differences (a real-space method that is not variational) and the reciprocal-space plane-wave method which is fully variational. We find that a new definition of the finite differences method [P. Maragakis, J. Soler, and E. Kaxiras, Phys. Rev. B \textbf{64}, 193101 (2001)] satisfies one of the two properties of variational behaviour at the cost of larger errors than the conventional finite differences method. On the other hand, a technique which represents functions in a number of plane-waves which is independent of system size, follows closely the plane-wave method and therefore also the criteria for variational behaviour. Its application is only limited by the requirement of having functions strictly localised in regions of real-space but this is a characteristic of most modern real-space methods as they are designed to have a computational cost that scales linearly with system size.

cond-mat.mtrl-sci↗

arXiv2001

Accurate kinetic energy evaluation in electronic structure calculations with localised functions on real space grids

We present a method for calculating the kinetic energy of localised functions represented on a regular real space grid. This method uses fast Fourier transforms applied to restricted regions commensurate with the simulation cell and is applicable to grids of any symmetry. In the limit of large systems it scales linearly with system size. Comparison with the finite difference approach shows that our method offers significant improvements in accuracy without loss of efficiency.

cond-mat.mtrl-sci↗