arXiv subjects

Mike C. Payne

Publications and source records attributed to Mike C. Payne.

24 records · Page 2Linked to original sources

arXiv2008

Development of a Classical Force Field for the Oxidised Si Surface: Application to Hydrophilic Wafer Bonding

We have developed a classical two- and three-body interaction potential to simulate the hydroxylated, natively oxidised Si surface in contact with water solutions, based on the combination and extension of the Stillinger-Weber potential and of a potential originally developed to simulate SiO2 polymorphs. The potential parameters are chosen to reproduce the structure, charge distribution, tensile surface stress and interactions with single water molecules of a natively oxidised Si surface model previously obtained by means of accurate density functional theory simulations. We have applied the potential to the case of hydrophilic silicon wafer bonding at room temperature, revealing maximum room temperature work of adhesion values for natively oxidised and amorphous silica surfaces of 97 mJ/m2 and 90mJ/m2, respectively, at a water adsorption coverage of approximately 1 monolayer. The difference arises from the stronger interaction of the natively oxidised surface with liquid water, resulting in a higher heat of immersion (203 mJ/m2 vs. 166 mJ/m2), and may be explained in terms of the more pronounced water structuring close to the surface in alternating layers of larger and smaller density with respect to the liquid bulk. The computed force-displacement bonding curves may be a useful input for cohesive zone models where both the topographic details of the surfaces and the dependence of the attractive force on the initial surface separation and wetting can be taken into account.

cond-mat.mtrl-sci↗

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↗

arXiv1995

The Static, Dynamic and Electronic Properties of Liquid Gallium Studied by First-Principles Simulation

First-principles molecular dynamics simulations having a duration of 8 ps have been used to study the static, dynamic and electronic properties of l-Ga at the temperatures 702 K and 982 K. The simulations use the density-functional pseudopotential method and the system is maintained on the Born-Oppenheimer surface by conjugate gradients relaxation. The static structure factor and radial distribution function of the simulated system agree very closely with experimental data, but the diffusion coefficient is noticeably lower than measured values. The long simulations allow us to calculate the dynamical structure factor $S(q,ω)$. A sound-wave peak is clearly visible in $S(q,ω)$ at small wavevectors, and we present results for the dispersion curve and hence the sound velocity, which is close to the experimental value. The electronic density of states is very close to the free-electron form. Values of the electrical conductivity calculated from Kubo-Greenwood formula are in satisfactory accord with measured data.

mtrl-th↗