Reactive Force Field for Proton Diffusion in BaZrO3 using an empirical valence bond approach

A new reactive force field to describe proton diffusion within the solid-oxide fuel cell material BaZrO3 has been derived. Using a quantum mechanical potential energy surface, the parameters of an interatomic potential model to describe hydroxyl groups within both pure and yttrium-doped BaZrO3 have been determined. Reactivity is then incorporated through the use of the empirical valence bond model. Molecular dynamics simulations (EVB-MD) have been performed to explore the diffusion of hydrogen using a stochastic thermostat and barostat whose equations are extended to the isostress-isothermal ensemble. In the low concentration limit, the presence of yttrium is found not to significantly influence the diffusivity of hydrogen, despite the proton having a longer residence time at oxygen adjacent to the dopant. This lack of influence is due to the fact that trapping occurs infrequently, even when the proton diffuses through octahedra adjacent to the dopant. The activation energy for diffusion is found to be 0.42 eV, in good agreement with experimental values, though the prefactor is slightly underestimated.Comment: Corrected titl

A new route towards uniformly functionalized single-layer graphene

It is shown, by DFT calculations, that the uniform functionalization of upper layer of graphite by hydrogen or fluorine does not change essentially its bonding energy with the underlying layers, whereas the functionalization by phenyl groups decreases the bonding energy by a factor of approximately ten. This means that the functionalized monolayer in the latter case can be easily separated by mild sonication. According to our computational results, such layers can be cleaned up to pure graphene, as well as functionalized further up to 25% coverage, without essential difficulties. The energy gap within the interval from 0.5 to 3 eV can be obtained by such one-side funtionalization using different chemical species.Comment: 15 pages, 3 figures, to appear in J. Phys. D: Applied Physic

Fast computation of the Kohn-Sham susceptibility of large systems

For hybrid systems, such as molecules grafted onto solid surfaces, the calculation of linear response in time dependent density functional theory is slowed down by the need to calculate, in N^4 operations, the susceptibility of N non interacting Kohn-Sham reference electrons. We show how this susceptibility can be calculated N times faster within finite precision. By itself or in combination with previous methods, this should facilitate the calculation of TDDFT response and optical spectra of hybrid systems.Comment: submitted 25/1/200

Recovering hidden Bloch character: Unfolding Electrons, Phonons, and Slabs

For a quantum state, or classical harmonic normal mode, of a system of spatial periodicity "R", Bloch character is encoded in a wavevector "K". One can ask whether this state has partial Bloch character "k" corresponding to a finer scale of periodicity "r". Answering this is called "unfolding." A theorem is proven that yields a mathematically clear prescription for unfolding, by examining translational properties of the state, requiring no "reference states" or basis functions with the finer periodicity (r,k). A question then arises, how should one assign partial Bloch character to a state of a finite system? A slab, finite in one direction, is used as the example. Perpendicular components k_z of the wavevector are not explicitly defined, but may be hidden in the state (and eigenvector |i>.) A prescription for extracting k_z is offered and tested. An idealized silicon (111) surface is used as the example. Slab-unfolding reveals surface-localized states and resonances which were not evident from dispersion curves alone.Comment: 11 pages, 7 figure

Modelling of epitaxial graphene functionalization

A new model for graphene, epitaxially grown on silicon carbide is proposed. Density functional theory modelling of epitaxial graphene functionalization by hydrogen, fluorine and phenyl groups has been performed with hydrogen and fluorine showing a high probability of cluster formation in high adatom concentration. It has also been shown that the clusterization of fluorine adatoms provides midgap states in formation due to significant flat distortion of graphene. The functionalization of epitaxial graphene using larger species (methyl and phenyl groups) renders cluster formation impossible, due to the steric effect and results in uniform coverage with the energy gap opening.Comment: 15 pages, 4 figures, to appear in Nanotechnolog

Stability, Adsorption and Diffusion of CH4, CO2 and H2 in Clathrate Hydrates

We present a study of the adsorption and diffusion of CH4, CO2 and H2 molecules in clathrate hydrates using ab initio van der Waals density functional formalism [Dion et al. Phys. Rev. Lett. 92, 246401 (2004)]. We find that the adsorption energy is dominated by van der Waals interactions and that, without them, gas hydrates would not be stable. We calculate the maximum adsorption capacity as well as the maximum hydrocarbon size that can be adsorbed.The relaxation of the host lattice is essential for a good description of the diffusion activation energies, which are estimated to be of the order of 0.2, 0.4, and 1.0 eV for H2, CO2, and CH4, respectively.Comment: 4 pages, 4 figures, 3 table

Electronic structure interpolation via atomic orbitals

We present an efficient scheme for accurate electronic structure interpolations based on the systematically improvable optimized atomic orbitals. The atomic orbitals are generated by minimizing the spillage value between the atomic basis calculations and the converged plane wave basis calculations on some coarse $k$-point grid. They are then used to calculate the band structure of the full Brillouin zone using the linear combination of atomic orbitals (LCAO) algorithms. We find that usually 16 -- 25 orbitals per atom can give an accuracy of about 10 meV compared to the full {\it ab initio} calculations. The current scheme has several advantages over the existing interpolation schemes. The scheme is easy to implement and robust which works equally well for metallic systems and systems with complex band structures. Furthermore, the atomic orbitals have much better transferability than the Shirley's basis and Wannier functions, which is very useful for the perturbation calculations

Evidence-based rules from family practice to inform family practice; The learning healthcare system case study on urinary tract infections

Background: Analysis of encounter data relevant to the diagnostic process sourced from routine electronic medical record (EMR) databases represents a classic example of the concept of a learning healthcare system (LHS). By collecting International Classification of Primary Care (ICPC) coded EMR data as part of the Transition Project from Dutch and Maltese databases (using the EMR TransHIS), data mining algorithms can empirically quantify the relationships of all presenting reasons for encounter (RfEs) and recorded diagnostic outcomes. We have specifically looked at new episodes of care (EoC) for two urinary system infections: simple urinary tract infection (UTI, ICPC code: U71) and pyelonephritis (ICPC code: U70). Methods: Participating family doctors (FDs) recorded details of all their patient contacts in an EoC structure using the ICPC, including RfEs presented by the patient, and the FDs' diagnostic labels. The relationships between RfEs and episode titles were studied using probabilistic and data mining methods as part of the TRANSFoRm project. Results: The Dutch data indicated that the presence of RfE's "Cystitis/Urinary Tract Infection", "Dysuria", "Fear of UTI", "Urinary frequency/urgency", "Haematuria", "Urine symptom/complaint, other" are all strong, reliable, predictors for the diagnosis "Cystitis/Urinary Tract Infection". The Maltese data indicated that the presence of RfE's "Dysuria", "Urinary frequency/urgency", "Haematuria" are all strong, reliable, predictors for the diagnosis "Cystitis/Urinary Tract Infection". The Dutch data indicated that the presence of RfE's "Flank/axilla symptom/complaint", "Dysuria", "Fever", "Cystitis/Urinary Tract Infection", "Abdominal pain/cramps general" are all strong, reliable, predictors for the diagnosis "Pyelonephritis". The Maltese data set did not present any clinically and statistically significant predictors for pyelonephritis. Conclusions: We describe clinically and statistically significant diagnostic associations observed between UTIs and pyelonephritis presenting as a new problem in family practice, and all associated RfEs, and demonstrate that the significant diagnostic cues obtained are consistent with the literature. We conclude that it is possible to generate clinically meaningful diagnostic evidence from electronic sources of patient data

Emergence of hierarchical networks and polysynchronous behaviour in simple adaptive systems

We describe the dynamics of a simple adaptive network. The network architecture evolves to a number of disconnected components on which the dynamics is characterized by the possibility of differently synchronized nodes within the same network (polysynchronous states). These systems may have implications for the evolutionary emergence of polysynchrony and hierarchical networks in physical or biological systems modeled by adaptive networks.Comment: 4 pages, 4 figure

Accuracy control in ultra-large-scale electronic structure calculation

Numerical aspects are investigated in ultra-large-scale electronic structure calculation. Accuracy control methods in process (molecular-dynamics) calculation are focused. Flexible control methods are proposed so as to control variational freedoms, automatically at each time step, within the framework of generalized Wannier state theory. The method is demonstrated in silicon cleavage simulation with 10^2-10^5 atoms. The idea is of general importance among process calculations and is also used in Krylov subspace theory, another large-scale-calculation theory.Comment: 8 pages, 3 figures. To appear in J.Phys. Condens. Matter. A preprint PDF file in better graphics is available at http://fujimac.t.u-tokyo.ac.jp/lses/index_e.htm