A model for time-dependent grain boundary diffusion of ions and electrons through a film or scale, with an application to alumina

A model for ionic and electronic grain boundary transport through thin films, scales or membranes with columnar grain structure is introduced. The grain structure is idealized as a lattice of identical hexagonal cells - a honeycomb pattern. Reactions with the environment constitute the boundary conditions and drive the transport between the surfaces. Time-dependent simulations solving the Poisson equation self-consistently with the Nernst-Planck flux equations for the mobile species are performed. In the resulting Poisson-Nernst-Planck system of equations, the electrostatic potential is obtained from the Poisson equation in its integral form by summation. The model is used to interpret alumina membrane oxygen permeation experiments, in which different oxygen gas pressures are applied at opposite membrane surfaces and the resulting flux of oxygen molecules through the membrane is measured. Simulation results involving four mobile species, charged aluminum and oxygen vacancies, electrons, and holes, provide a complete description of the measurements and insight into the microscopic processes underpinning the oxygen permeation of the membrane. Most notably, the hypothesized transition between p-type and n-type ionic conductivity of the alumina grain boundaries as a function of the applied oxygen gas pressure is observed in the simulations. The range of validity of a simple analytic model for the oxygen permeation rate, similar to the Wagner theory of metal oxidation, is quantified by comparison to the numeric simulations. The three-dimensional model we develop here is readily adaptable to problems such as transport in a solid state electrode, or corrosion scale growth

Automatic Generation of Matrix Element Derivatives for Tight Binding Models

Tight binding (TB) models are one approach to the quantum mechanical many particle problem. An important role in TB models is played by hopping and overlap matrix elements between the orbitals on two atoms, which of course depend on the relative positions of the atoms involved. This dependence can be expressed with the help of Slater-Koster parameters, which are usually taken from tables. Recently, a way to generate these tables automatically was published. If TB approaches are applied to simulations of the dynamics of a system, also derivatives of matrix elements can appear. In this work we give general expressions for first and second derivatives of such matrix elements. Implemented in a computer program they obviate the need to type all the required derivatives of all occuring matrix elements by hand.Comment: 11 pages, 2 figure

Enteral nutrition in the critically ill: A prospective survey in an Australian intensive care unit

Publisher's copy made available with the permission of the publisher © Australian Society of AnaesthetistsNutritional support is routine practice in critically ill patients and enteral feeding is preferred to the parenteral route. However this direct delivery of nutrients to the gut is potentially ineffective for a variety of reasons. We performed a prospective audit of 40 consecutive intensive care patients to determine whether enteral feeding met the nutritional requirements of our patients. The ideal requirements for each patient were calculated using the Harris-Benedict equation with an adjustment determined by the patient’s diagnosis. We compared the amount of feed delivered with the daily requirements over a seven-day period. Successful feeding was defined as the achievement of 90% of the ideal calorie requirement for two consecutive days. The mean calculated (±SD) energy requirement was 9566kJ (±2586). Patients received only 51% (SD 38) of their energy requirements throughout the study period. Only 10 patients (25%)were successfully fed for at least any two-day period in the seven days. Feeding was limited mainly by gastrointestinal dysfunction or by the need to fast the patient for medical, surgical and airway procedures. Success of feeding was not related to the use of sedative or paralysing agents and had no correlation with plasma albumin concentration. There was no difference in the volume of feed delivered to patients who survived or died. Prokinetic agents were used in 25 patients and in these patients there was a trend towards improved delivery of feed.I. De Beaux, M. Chapman, R. Fraser, M. Finnis, B. De Keulenaer, D. Liberalli, M. Satanekhttp://www.aaic.net.au/Article.asp?D=200111

Stress induced hyperglycemia and the subsequent risk of type 2 diabetes in survivors of critical illness

OBJECTIVE: Stress induced hyperglycemia occurs in critically ill patients who have normal glucose tolerance following resolution of their acute illness. The objective was to evaluate the association between stress induced hyperglycemia and incident diabetes in survivors of critical illness. DESIGN: Retrospective cohort study. SETTING: All adult patients surviving admission to a public hospital intensive care unit (ICU) in South Australia between 2004 and 2011. PATIENTS: Stress induced hyperglycemia was defined as a blood glucose ≥ 11.1 mmol/L (200 mg/dL) within 24 hours of ICU admission. Prevalent diabetes was identified through ICD-10 coding or prior registration with the Australian National Diabetes Service Scheme (NDSS). Incident diabetes was identified as NDSS registration beyond 30 days after hospital discharge until July 2015. The predicted risk of developing diabetes was described as sub-hazard ratios using competing risk regression. Survival was assessed using Cox proportional hazards regression. MAIN RESULTS: Stress induced hyperglycemia was identified in 2,883 (17%) of 17,074 patients without diabetes. The incidence of type 2 diabetes following critical illness was 4.8% (821 of 17,074). The risk of diabetes in patients with stress induced hyperglycemia was approximately double that of those without (HR 1.91 (95% CI 1.62, 2.26), p<0.001) and was sustained regardless of age or severity of illness. CONCLUSIONS: Stress induced hyperglycemia identifies patients at subsequent risk of incident diabetes.Mark P. Plummer, Mark E. Finnis, Liza K. Phillips, Palash Kar, Shailesh Bihari, Vishwanath Biradar, Stewart Moodie, Michael Horowitz, Jonathan E. Shaw, Adam M. Dean

Gaussian Approximation Potentials: the accuracy of quantum mechanics, without the electrons

We introduce a class of interatomic potential models that can be automatically generated from data consisting of the energies and forces experienced by atoms, derived from quantum mechanical calculations. The resulting model does not have a fixed functional form and hence is capable of modeling complex potential energy landscapes. It is systematically improvable with more data. We apply the method to bulk carbon, silicon and germanium and test it by calculating properties of the crystals at high temperatures. Using the interatomic potential to generate the long molecular dynamics trajectories required for such calculations saves orders of magnitude in computational cost.Comment: v3-4: added new material and reference

Development of a tight-binding potential for bcc-Zr. Application to the study of vibrational properties

We present a tight-binding potential based on the moment expansion of the density of states, which includes up to the fifth moment. The potential is fitted to bcc and hcp Zr and it is applied to the computation of vibrational properties of bcc-Zr. In particular, we compute the isothermal elastic constants in the temperature range 1200K < T < 2000K by means of standard Monte Carlo simulation techniques. The agreement with experimental results is satisfactory, especially in the case of the stability of the lattice with respect to the shear associated with C'. However, the temperature decrease of the Cauchy pressure is not reproduced. The T=0K phonon frequencies of bcc-Zr are also computed. The potential predicts several instabilities of the bcc structure, and a crossing of the longitudinal and transverse modes in the (001) direction. This is in agreement with recent ab initio calculations in Sc, Ti, Hf, and La.Comment: 14 pages, 6 tables, 4 figures, revtex; the kinetic term of the isothermal elastic constants has been corrected (Eq. (4.1), Table VI and Figure 4

A simple environment-dependent overlap potential and Cauchy violation in solid argon

We develop an analytic and environment-dependent interatomic potential for the overlap repulsion in solid argon, based on an approximate treatment of the non-orthogonal Tight-Binding theory for the closed-shell systems. The present model can well reproduce the observed elastic properties of solid argon including Cauchy violation at high pressures, yet very simple. A useful and novel analysis is given to show how the elastic properties are related to the environment-dependence incorporated into a generic pairwise potential. The present study has a close link to the broad field of computational materials science, in which the inclusion of environment dependence in short-ranged repulsive part of a potential model is sometimes crucial in predicting the elastic properties correctly.Comment: 10 pages, 3 figure

Stress hyperglycaemia in critically ill patients and the subsequent risk of diabetes: a systematic review and meta-analysis.

Hyperglycaemia occurs frequently in critically ill patients without diabetes. We conducted a systematic review and meta-analysis to evaluate whether this 'stress hyperglycaemia' identifies survivors of critical illness at increased risk of subsequently developing diabetes.We searched the MEDLINE and Embase databases from their inception to February 2016. We included observational studies evaluating adults admitted to the intensive care unit (ICU) who developed stress hyperglycaemia if the researchers reported incident diabetes or prediabetes diagnosed ≥3 months after hospital discharge. Two reviewers independently screened the titles and abstracts of identified studies and evaluated the full text of relevant studies. Data were extracted using pre-defined data fields, and risk of bias was assessed using the Newcastle-Ottawa Scale. Pooled ORs with 95 % CIs for the occurrence of diabetes were calculated using a random-effects model.Four cohort studies provided 2923 participants, including 698 with stress hyperglycaemia and 131 cases of newly diagnosed diabetes. Stress hyperglycaemia was associated with increased risk of incident diabetes (OR 3.48; 95 % CI 2.02-5.98; I (2)  = 36.5 %). Studies differed with regard to definitions of stress hyperglycaemia, follow-up and cohorts studied.Stress hyperglycaemia during ICU admission is associated with increased risk of incident diabetes. The strength of this association remains uncertain because of statistical and clinical heterogeneity among the included studies.Yasmine Ali Abdelhamid, Palash Kar, Mark E. Finnis, Liza K. Phillips, Mark P. Plummer, Jonathan E. Shaw, Michael Horowitz and Adam M. Dean

The MOLDY short-range molecular dynamics package

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy