Quantitative LEED I-V and ab initio study of the Si(111)-3x2-Sm surface structure and the missing half order spots in the 3x1 diffraction pattern

We have used Low Energy Electron Diffraction (LEED) I-V analysis and ab initio calculations to quantitatively determine the honeycomb chain model structure for the Si(111)-3x2-Sm surface. This structure and a similar 3x1 recontruction have been observed for many Alkali-Earth and Rare-Earth metals on the Si(111) surface. Our ab initio calculations show that there are two almost degenerate sites for the Sm atom in the unit cell and the LEED I-V analysis reveals that an admixture of the two in a ratio that slightly favours the site with the lower energy is the best match to experiment. We show that the I-V curves are insensitive to the presence of the Sm atom and that this results in a very low intensity for the half order spots which might explain the appearance of a 3x1 LEED pattern produced by all of the structures with a 3x2 unit cell.Comment: 10 pages, 13 figures. Preliminary work presented at the the APS March meeting, Baltimore MD, 2006. To be published in Phys. Rev. B. April/May 200

Improved real-space genetic algorithm for crystal structure and polymorph prediction

Existing genetic algorithms for crystal structure and polymorph prediction can suffer from stagnation during evolution, with a consequent loss of efficiency and accuracy. An improved genetic algorithm is introduced herein which penalizes similar structures and so enhances structural diversity in the population at each generation. This is shown to improve the quality of results found for the theoretical prediction of simple model crystal structures. In particular, this method is demonstrated to find three new zero-temperature phases of the Dzugutov potential that have not been previously reported

STM and ab initio study of holmium nanowires on a Ge(111) Surface

A nanorod structure has been observed on the Ho/Ge(111) surface using scanning tunneling microscopy (STM). The rods do not require patterning of the surface or defects such as step edges in order to grow as is the case for nanorods on Si(111). At low holmium coverage the nanorods exist as isolated nanostructures while at high coverage they form a periodic 5x1 structure. We propose a structural model for the 5x1 unit cell and show using an ab initio calculation that the STM profile of our model structure compares favorably to that obtained experimentally for both filled and empty states sampling. The calculated local density of states shows that the nanorod is metallic in character.Comment: 4 pages, 12 figures (inc. subfigures). Presented at the the APS March meeting, Baltimore MD, 200

Reshaping graduate outcomes of science students – The contribution of undergraduate research experiences

Today’s science graduates require substantially different skills compared to yesterday’s graduates given the changing nature of modern science. As higher education institutions struggle to reform curricula and pedagogy, undergraduate research experiences (UREs) are increasingly being incorporated to enhance undergraduate science curricula. This study is situated within a traditional Bachelor of Science degree that offers students some voluntary opportunities to participate in UREs. This study explores two graduating science cohorts (n=272), comparing those who did and did not participate in UREs. A survey investigated student perceptions (importance, confidence and improvements) of five graduate outcomes in the context of science: writing skills, communication skills, quantitative skills (QS), teamwork skills and content knowledge. Cross-tabs and a linear discriminant analysis were used to investigate perception change between the two groups. The notable differences in perception scores in this study were consistently higher in QS, perhaps indicative of UREs emphasising the need for such skills in science or from students gaining increased confidence as a result of utilising QS within an authentic context. Our results reveal little difference in other student outcome areas, which raises questions around the role of UREs as a broad strategy for enhancing the achievement of graduate outcomes in science. This study is limited to a single institution and is focused on specific graduate outcomes, so only limited conclusions can be drawn. However, further research to determine the graduate outcomes gained from UREs would benefit the sector, particularly science disciplines, in the changing focus of government policy on student learning outcomes

Evaluation of a Liquid Amine System for Spacecraft Carbon Dioxide Control

The analytical and experimental studies are described which were directed toward the acquisition of basic information on utilizing a liquid amine sorbent for in use in a CO2 removal system for manned spacecraft. Liquid amine systems are successfully used on submarines for control of CO2 generated by the crew, but liquid amines were not previously considered for spacecraft applications due to lack of development of satisfactory rotary phase separators. Developments in this area now make consideration of liquid amines practical for spacecraft system CO2 removal. The following major tasks were performed to evaluate liquid amine systems for spacecraft: (1) characterization, through testing, of the basic physical and thermodynamic properties of the amine solution; (2) determination of the dynamic characteristics of a cocurrent flow absorber; and (3) evaluation, synthesis, and selection of a liquid amine system concept oriented toward low power requirements. A low weight, low power system concept was developed. Numerical and graphical data are accompanied by pertinent observations

Atomistic Molecular Dynamics Simulations of Shock Compressed Quartz

Atomistic non-equilibrium molecular dynamics (NEMD) simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer and van Santen to construct the Hugoniot of quartz. Our scheme mimics the real world experimental set up by using a flyer-plate impactor to initiate the shock wave and is the first shock wave simulation that uses a geom- etry optimised system of a polar slab in a 3-dimensional system employing periodic boundary conditions. Our scheme also includes the relaxation of the surface dipole in the polar quartz slab which is an essential pre-requisite to a stable simulation. The original BKS potential is unsuited to shock wave calculations and so we propose a simple modification. With this modification, we find that our calculated Hugoniot is in good agreement with experimental shock wave data up to 25 GPa, but significantly diverges beyond this point. We conclude that our modified BKS potential is suitable for quartz under representative pressure conditions of the Earth core, but unsuitable for high-pressure shock wave simulations. We also find that the BKS potential incorrectly prefers the {\beta}-quartz phase over the {\alpha}-quartz phase at zero-temperature, and that there is a {\beta} \rightarrow {\alpha} phase-transition at 6 GPa.Comment: 19 pages, 13 figures, Accepted for publication in Journal of Chemical Physic

Oral iron exacerbates colitis and influences the intestinal microbiome

Inflammatory bowel disease (IBD) is associated with anaemia and oral iron replacement to correct this can be problematic, intensifying inflammation and tissue damage. The intestinal microbiota also plays a key role in the pathogenesis of IBD, and iron supplementation likely influences gut bacterial diversity in patients with IBD. Here, we assessed the impact of dietary iron, using chow diets containing either 100, 200 or 400 ppm, fed ad libitum to adult female C57BL/6 mice in the presence or absence of colitis induced using dextran sulfate sodium (DSS), on (i) clinical and histological severity of acute DSS-induced colitis, and (ii) faecal microbial diversity, as assessed by sequencing the V4 region of 16S rRNA. Increasing or decreasing dietary iron concentration from the standard 200 ppm exacerbated both clinical and histological severity of DSS-induced colitis. DSS-treated mice provided only half the standard levels of iron ad libitum (i.e. chow containing 100 ppm iron) lost more body weight than those receiving double the amount of standard iron (i.e. 400 ppm); p<0.01. Faecal calprotectin levels were significantly increased in the presence of colitis in those consuming 100 ppm iron at day 8 (5.94-fold) versus day-10 group (4.14-fold) (p<0.05), and for the 400 ppm day-8 group (8.17-fold) versus day-10 group (4.44-fold) (p<0.001). In the presence of colitis, dietary iron at 400 ppm resulted in a significant reduction in faecal abundance of Firmicutes and Bacteroidetes, and increase of Proteobacteria, changes which were not observed with lower dietary intake of iron at 100 ppm. Overall, altering dietary iron intake exacerbated DSS-induced colitis; increasing the iron content of the diet also led to changes in intestinal bacteria diversity and composition after colitis was induced with DSS

Identification and Characterisation of an Iron-Responsive Candidate Probiotic

Background: Iron is an essential cofactor in almost all biological systems. The lactic acid bacteria (LAB), frequently employed as probiotics, are unusual in having little or no requirement for iron. Iron in the human body is sequestered by transferrins and lactoferrin, limiting bacterial growth. An increase in the availability of iron in the intestine by bleeding, surgery, or under stress leads to an increase in the growth and virulence of many pathogens. Under these high iron conditions, LAB are rapidly out-competed; for the levels of probiotic bacteria to be maintained under high iron conditions they must be able to respond by increasing growth rate to compete with the normal flora. Despite this, iron-responsive genera are poorly characterised as probiotics. Methodology/Principal Findings: Here, we show that a panel of probiotics are not able to respond to increased iron availability, and identify an isolate of Streptococcus thermophilus that can increase growth rate in response to increased iron availability. The isolate of S. thermophilus selected was able to reduce epithelial cell death as well as NF-kB signalling and IL-8 production triggered by pathogens. It was capable of crossing an epithelial cell barrier in conjunction with E. coli and downregulating Th1 and Th17 responses in primary human intestinal leukocytes. Conclusions/Significance: We propose that an inability to compete with potential pathogens under conditions of high iron availability such as stress and trauma may contribute to the lack of efficacy of many LAB-based probiotics in treatin

Testing the APSIM model with data from a phosphorus and nitrogen replenishment experiment on an oxisol in

Abstract An experiment was conducted on an Oxisol near Maseno in western Kenya, to compare the growth of maize crops to inputs of two phosphorus sources. Commercial triple superphosphate (TSP) and Minjingu phosphate rock were applied either at a once-only rate of 250 kg P ha -1 or as five annual inputs of 50 kg P ha -1 . The experiment was carried out over 10 cropping seasons between 1996 and 2000. An additional factor studied was the source of N, either as urea or tithonia biomass-N to supply 60 kg N ha -1 . Both N and P sources were applied only to the crops grown in the long rain season. The APSIM model has been tested against this data set. The effects of P treatments were large in the long rain season, but in the short rain season the inadequate supply of N greatly reduced growth and P effects. The yields of the maize crops were predicted well (r 2 = 0.88) with respect to both the P treatments (as TSP) and the N inputs (as urea). The predicted water, N and P stresses were informative in understanding the contrasting pattern of response observed in the two seasons. The simulation of this long-term experiment shows that the APSIM SoilP module is robust, in as much as it extends the testing of the model to a very different environment where there were both N and P stresses affecting plant growth, and on a very different soil type to where the concepts in the APSIM phosphorus routines were originally developed and tested. Crop production on many soils in western Kenya is limited by both nitrogen (N) and phosphorus (P). The concept of recapitalisation of soil P has focused attention on the use of rock phosphate materials rather than commercial forms of processed fertilisers, and the feasibility of raising soil P through large, one-time application rather than a gradual increase with smaller, but regular inputs . Such strategies have been evaluated in long-term experiments in western Kenya. Probert In this paper, we describe the testing of the APSIM P routines using an experiment that provides suitable data for testing some aspects of the model. The annual rainfall and soil type, especially with regards to its phosphorus sorption properties, ar