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

Trigonal to pentagonal bipyramidal coordination switching in a Co(II) single-ion magnet

In molecular magnetism and single-ion magnets in particular, the observation of slow relaxation of the magnetization is intimately linked to the coordination environment of the metal center. Such systems typically have blocking temperatures well below that of liquid nitrogen, and therefore detailed magnetic characterization is usually carried out at very low temperatures. Despite this, there has been little advantage taken of ultralow temperature single-crystal X-ray diffraction techniques that could provide a full understanding of the crystal structure in the same temperature regime where slow magnetic relaxation occurs. Here, we present a systematic variable temperature single crystal X-ray diffraction study of [CoII(NO3)3(H2O)(HDABCO)] (1) {DABCO = 1,4-diazabicyclo[2.2.2]octane} conducted between 295 to 4 K. A reversible and robust disorder-to-order, single-crystal to single-crystal phase transition was identified, which accompanied a switching of the coordination geometry around the central Co(II) from 5- to 7-coordinate below 140 K. The magnetic properties were investigated, revealing slow relaxation of the magnetization arising from a large easy-plane magnetic anisotropy (+D) in the Co(II) pentagonal bipyramidal environment observed at low temperatures. This study highlights the importance of conducting thorough low temperature crystallographic studies, particularly where magnetic characterization is carried out at such low temperatures

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

Two alternative approaches to access mixed hydride-amido zinc complexes : synthetic, structural and solution implications

Using bis(amide) Zn(HMDS)2 (HMDS = 1,1,1,3,3,3-hexamethyldisilazide) as a precursor, this study explores the synthesis of N-heterocyclic carbene stabilized mixed amido-hydride zinc complexes using two alternative hydride sources, namely dimethylamine borane (DMAB) and phenylsilane PhSiH3. Hydride-rich zinc cluster Zn4(HMDS)2H6·2IPr (1) (IPr = 1,3-bis(2,6-di-isopropylphenyl)imidazol-2-ylidene), which can be envisaged as a co-complex of IPr·ZnH2 and (HMDS)ZnH, is obtained when DMAB is employed, with the concomitant formation of heteroleptic bis(amido)borane [HB(NMe2)(HMDS)] and H2 evolution. NMR studies in d8-THF show that although the bulky carbene IPr does not bind to the zinc bis(amide), its presence in the reaction media is required in order to stabilise 1. Reactions using the slightly less sterically demanding NHC IXy (IXy = 1,3-bis-(2,6-dimethylphenyl)imidazol-2-ylidene) led to the isolation and structural elucidation of the carbene adduct Zn(HMDS)2·IXy (2). Contrastingly, mixtures of equimolar amounts of PhSiH3 and the zinc bis(amide) (60 °C, 3 h, hexane) afforded monomeric heteroleptic hydride (HMDS)ZnH·IPr (3). NMR studies, including DOSY experiments, revealed that while the integrity of 3 is retained in polar d8-THF solutions, in lower polarity C6D6 it displays a much more complex solution behaviour, being in equilibrium with the homoleptic species ZnH2·IPr, Zn(HMDS)2 and IPr

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

Collecting biological material from palliative care patients in the last weeks of life: a feasibility study

Objective To assess the feasibility of prospectively collecting biological samples (urine) from palliative care patients in the last weeks of life. Setting A 30-bedded specialist hospice in the North West of England. Participants Participants were adults with a diagnosis of advanced disease and able to provide written informed consent. Method Potential participants were identified by a senior clinician over a 12-week period in 2014. They were then approached by a researcher and invited to participate according to a developed recruitment protocol. Outcomes Feasibility targets included a recruitment rate of 50%, with successful collection of samples from 80% who consented. Results A total of 58 patients were approached and 33 consented (57% recruitment rate). Twenty-five patients (43%) were unable to participate or declined; 10 (17%) became unwell, too fatigued, lost capacity, died or were discharged home; and 15 (26%) refused, usually these patients had distressing pain, low mood or profound fatigue. From the 33 recruited, 20 participants provided 128 separate urine samples, 12 participants did not meet the inclusion criteria at the time of consent and 1 participant was unable to provide a sample. The criterion for a urinary catheter was removed for the latter 6 weeks. The collection rate during the first 6 weeks was 29% and 93% for the latter 6 weeks. Seven people died while the study was ongoing, and another 4 participants died in the following 4 weeks. Conclusions It is possible to recruit and collect multiple biological samples over time from palliative care patients in the last weeks and days of life even if they have lost capacity. Research into the biological changes at the end of life could develop a greater understanding of the biology of the dying process. This may lead to improved prognostication and care of patients towards the end of life

A study of volatile compounds in the breath of children with type 1 diabetes

A pilot study of exhaled volatile compounds and their correlation with blood glucose levels in eight children with type 1 diabetes is reported. Five paired blood and breath samples were obtained from each child over a 6 hour period. The blood glucose concentration ranged from 41.4 to 435.6 mg/dL. Breath samples were collected in Tedlar bags and immediately evacuated through thermal desorption tubes packed with Carbopack B and C. The VOCs were later recovered by thermal desorption and analysed using gas chromatography mass spectrometry. The study identified 74 volatile compounds present in at least 10% of the patient samples. Of these 74 volatiles 36 were found in all patient samples tested. Further analysis of the 36 compounds found that none showed significant overall correlation with blood glucose levels. Isoprene showed a weak negative correlation with blood glucose levels. Acetone was found to have no correlation with blood glucose levels for the patients studied. Some patients showed significant individual correlation between the relative peak areas of certain compounds and blood glucose levels. However, there was no consistent pattern observed within these results across all 8 patients. Additional breath samples were collected in Tedlar bags and analysed using SIFTMS for 3 of the patients and a healthy control. The levels of 24 volatiles are reported and were found to be generally consistent with previously reported SIFT-MS data. In agreement with the GCMS data, no compounds exhibited a significant overall correlation with blood glucose level

A longitudinal study of the faecal microbiome and metabolome of periparturient mares

Periparturient mares are at increased risk of colic including large colon volvulus, which has a high mortality rate. Alterations in colonic microbiota related to either physiological or management changes, or both, that occur at this time have been suggested as potential causes for increased colic risk in this population of horses. Although the effect of management changes on the horse faecal microbiota has been investigated, limited work has been conducted to investigate changes in faecal microbiota structure and function in the periparturient period. The objectives of the current study were to investigate temporal stability of the faecal microbiota and volatile organic compounds (VOCs) of the faecal metabolome in periparturient mares

Modelling nitrogen mineralization from manures: representing quality aspects by varying C:N ratio of sub-pools

The mineralization/immobilization of nitrogen when organic sources are added to soil is represented in many simulation models as the outcome of decomposition of the added material and synthesis of soil organic matter. These models are able to capture the pattern of N release that is attributable to the N concentration of plant materials, or more generally the C:N ratio of the organic input. However, the models are unable to simulate the more complex pattern of N release that has been observed for some animal manures, notably materials that exhibit initial immobilization of N even when the C:N of the material suggests it should mineralize N. The APSIM SoilN module was modified so that the three pools that constitute added organic matter could be specified in terms of both the fraction of carbon in each pool and also their C:N ratios (previously it has been assumed that all pools have the same C:N ratio). It is shown that the revised model is better able to simulate the general patterns on N mineralized that has been reported for various organic sources. By associating the model parameters with measured properties (the pool that decomposes most rapidly equates with water-soluble C and N; the pool that decomposes slowest equates with lignin-C) the model performed better than the unmodified model in simulating the N mineralization from a range of feeds and faecal materials measured in an incubation experimen