Recent publications in Physical Sciences

Guo, Zhifang, Luu, Jenny, Blair, Victoria, Deacon, Glen B., and Junk, Peter C. (2019) Replacing mercury: syntheses of lanthanoid pyrazolates from free lanthanoid metals, pentafluorophenylsilver, and pyrazoles, aided by a facile synthesis of polyfluoroarylsilver compounds. European Journal of Inorganic Chemistry, 2019 (7). pp. 1018-1029.
The polyfluorophenylsilver complexes [Ag-2(C6F4Br-4)(2)(py)(3)] (py = pyridine) (1) and [{Ag2R2(py)(2)}(n)] [R = C6F5 (2); C6F4Br-3 (3); C6F4H-4 (4)] were prepared in reasonable yields by reactions of silver(I) oxide with the appropriate polyfluorobenzenes in pyridine. This simple and convenient synthesis is selective and does not lead to debromination of C6HF4Br-(3 or 4). Complex 1 is dinuclear with AgR2 and Ag(py)(3) units linked by a bridging polyfluoroaryl group and Ag center dot center dot center dot Ag interactions, whereas 2-4 are polymeric with alternating AgR2 and Ag(py)(2) units similarly linked. The trivalent lanthanoid pyrazolates, [Ln(Ph(2)pz)(3)(py)(2)]center dot 2thf (Ph(2)pz = 3,5-diphenylpyrazolate; Ln = Yb, 5, Er, 6, Dy, 7, Lu, 8; thf = tetrahydrofuran), [Ho(Ph(2)pz)(3)(py)(thf)] (9), [Ln(Ph(2)pz)(3)(py)(dme)]center dot solv (Ln = Tb, solv = 1.75PhMe, 10, Gd, solv = 1.5dme, 11; dme = 1,2-dimethoxyethane; PhMe = toluene), [Ln(Ph(2)pz)(3)(thf)(3)] (Ln = La, 12, Ce, 13, Nd, 14), [Ln(tBu(2)pz)(3)(py)(2)] (tBu(2)pz = 3,5-di-tert-butylpyrazolate; Ln = Yb, 15, Tm, 16, Ho, 17, Dy, 18), [Yb(Phtpz)(3)(py)(2)]center dot PhMe (19) (Phtpz = 3-Phenyl-5-(2 '-thienyl)pyrazolate) and [Nd(ttfpz)(3)(dme)(2)] (20) (ttfpz = 3-(2 '-thienyl)-5-(trifluoromethyl)pyrazolate) have been prepared by redox transmetallation/protolysis (RTP) reactions employing lanthanoid metals, pentafluorophenylsilver and the corresponding pyrazoles (pzH) in donor solvents. This is a new synthetic route in which AgC6F5 replaces the more commonly used Hg(C6F5)(2) or HgPh2. Yields are good to excellent if long crystallization times are used but the heavier Ln metals require activation with iodine to induce reaction. The monomeric structures exhibit eta(2)-bound pyrazolate ligands with eight-coordinate metal atoms for complexes 5-9 and 15-19, nine-coordinate metal atoms for complexes 10-14, and ten-coordinate metal atoms for complex 20.

Lawn, Julian A., and Kosov, Daniel S. (2019) Coupled elastic membranes model for quantum heat transport in semiconductor nanowires. European Physical Journal B: Condensed Matter and Complex Systems, 92 (2). 43.
Presented here is a nanowire model, consisting of coupled elastic membranes with the purpose of investigating thermal transport in quasi-one-dimensional quantum systems. The vibrations of each elastic membrane are quantized and the flow of the vibrational energy between adjacent membranes is allowed. The ends of the nanowire are attached to thermal baths held at different temperatures. We derived quantum master equation for energy flow across the nanowire and obtained thermal currents and other key observables. We study the effects of a disordered boundary on the thermal current by randomizing the membrane radii. We evaluate the model as a nanowire analogue as well as study the effects of a disordered boundary on thermal conductivity. The calculations show that the membrane lattice model demonstrates diameter phonon confinement and a severe reduction in thermal conductivity due to surface roughness which is characteristic of semiconductor nanowires. The surface roughness also produces a length dependence of the thermal conductivity of the form κ = αLβ, with β dependent on disorder characteristics, in the otherwise ballistic regime. Finally, the parameters of the model are fitted to available experimental data for silicon nanowires and the results of the calculations are assessed against the experimental data.

Kershaw, Vincent F., and Kosov, Daniel S. (2019) Non-equilibrium Green's function theory for non-adiabatic effects in quantum transport: inclusion of electron-electron interactions. Journal of Chemical Physics, 150. 074101.
Non-equilibrium Green's function theory for non-adiabatic effects in quantum transport [Kershaw and Kosov, J. Chem. Phys. 147, 224109 (2017) and J. Chem. Phys. 149, 044121 (2018)] is extended to the case of interacting electrons. We consider a general problem of quantum transport of interacting electrons through a central region with dynamically changing geometry. The approach is based on the separation of time scales in the non-equilibrium Green's functions and the use of the Wigner transformation to solve the Kadanoff-Baym equations. The Green's functions and correlation self-energy are non-adiabatically expanded up to the second order central time derivatives. We produce expressions for Green's functions with non-adiabatic corrections and a modified formula for electric current; both depend not only on instantaneous molecular junction geometry but also on nuclear velocities and accelerations. The theory is illustrated by the study of electron transport through a model single-resonant level molecular junction with local electron-electron repulsion and a dynamically changing geometry.

Werner, Daniel, Deacon, Glen B., and Junk, Peter C. (2019) Trapping CS₂²⁻ and S₃²⁻ between two ytterbium formamidinates. Inorganic Chemistry, 58 (3). pp. 1912-1918.
Treatment of [YbII(DippForm)2(thf)n] (n = 2 (1aYb), n = 1 (1bYb); DippForm = N,N′-bis(2,6-diisopropylphenyl)formamidinate), with either excess CS2 or S8 gives [YbIII2(DippForm)4(CS2)] (3) and [YbIII2(DippForm)4(S2)0.5/(S3)0.5] (4) respectively. 3 is a new addition to an exclusive class of compounds containing the CS22− dianion, and 4 is the first crystallographically characterized example of a rare-earth trisulfide complex.

de Bruin-Dickason, Caspar N., Deacon, Glen B., Jones, Cameron, Junk, Peter C., and Wiecko, Michal (2019) Functionalised alkaline earth iodides from Grignard synthons "PhAeI(thf)ₙ" (Ae = Mg‐Ba). European Journal of Inorganic Chemistry, 2019 (7). pp. 1030-1038.
Derivatisation of Grignard synthons "PhAeI(thf)(n)" (Ae = Mg-Ba) prepared in situ from reactions of metal filings and iodobenzene provides a one-pot synthesis of heteroleptic N donor alkaline earth iodide complexes. Protolysis of "PhAeI(thf)(n)" with 3,5-diphenylpyrazole (Ph(2)pzH) yields pyrazolate complexes [Mg-2(mu-Ph(2)pz)(2)(I)(2)(thf)(3)] (1), [Ae(Ph(2)pz)(I)(thf)(4)] (Ae = Ca (2), Sr (3)), and [Ba-2(Ph(2)pz)(2)(mu-I)(2)(thf)(8)] (4). Addition of the Ae-Ph moiety to carbodiimide MesN=C=NMes (Mes = 2,4,6-(CH3)(3)C6H2) gave a series of benzamidinate iodide complexes [Ca-2{(MesN)(2)CPh}(2)(mu-I)(2)(thf)(4)] (6), [Sr{(MesN)(2)CPh}(I)(thf)(4)] (7), and [{Ba{(MesN)(2)CPh}(mu-I)(thf)(3)}(infinity)] (8). By contrast a symmetrical magnesium complex [Mg{(MesN)(2)CPh}(2)(thf)] (5) was obtained by Schlenk redistribution. These syntheses proceed without pre-activation of the metal for strontium and barium, and after activation with 2 mol-% iodine for calcium. The heavy alkaline earth metal complexes are the first examples of heteroleptic halide pyrazolate or amidinate complexes for strontium and barium. Complexes 1, 3, 4 and 6-8 were characterised crystallographically, revealing diverse structural chemistry of heteroleptic amidinate and pyrazolate iodide complexes across the alkaline earth series. A highlight is [Ba{(MesN)(2)CPh}(mu-I)(thf)(3)](infinity) (8) - an iodide bridged infinite 1-D polymer.

Sanderson, Stephen, Philippa, Bronson, Vamvounis, George, Burn, Paul L., and White, Ronald D. (2019) Understanding charge transport in Ir(ppy)₃:CBP OLED films. Journal of Chemical Physics, 150 (9). 094110.
Ir(ppy)₃:CBP blends have been widely studied as the emissive layer in organic light emitting diodes (OLEDs), yet crucial questions about charge transport within the layer remain unaddressed. Recent molecular dynamics simulations show that the Ir(ppy)₃ molecules are not isolated from each other, but at concentrations of as low as 5 wt. % can be part of connected pathways. Such connectivity raises the question of how the iridium(iii) complexes contribute to long-range charge transport in the blend. We implement a kinetic Monte Carlo transport model to probe the guest concentration dependence of charge mobility and show that distinct minima appear at approximately 10 wt. % Ir(ppy)₃ due to an increased number of trap states that can include interconnected complexes within the blend film. The depth of the minima is shown to be dependent on the electric field and to vary between electrons and holes due to their different trapping depths arising from the different ionization potentials and electron affinities of the guest and host molecules. Typical guest-host OLEDs use a guest concentration below 10 wt. % to avoid triplet-triplet annihilation, so these results suggest that optimal device performance is achieved when there is significant charge trapping on the iridium(iii) complex guest molecules and minimum interactions of the emissive chromophores that can lead to triplet-triplet annihilation.

Bloomfield, Keith J., Prentice, I. Colin, Cernusak, Lucas A., Eamus, Derek, Medlyn, Belinda E., Rumman, Rizwana, Wright, Ian J., Boer, Matthias M., Cale, Peter, Cleverly, James, Egerton, John J.G., Ellsworth, David S., Evans, Bradley J., Hayes, Lucy S., Hutchinson, Michael F., Liddell, Michael J., Macfarlane, Craig, Meyer, Wayne S., Togashi, Henrique F., Wardlaw, Tim, Zhu, Lingling, and Atkin, Owen K. (2019) The validity of optimal leaf traits modelled on environmental conditions. New Phytologist, 221 (3). pp. 1409-1423.
The ratio of leaf intercellular to ambient CO2 (χ) is modulated by stomatal conductance (gs). These quantities link carbon (C) assimilation with transpiration, and along with photosynthetic capacities (Vcmax and Jmax) are required to model terrestrial C uptake. We use optimization criteria based on the growth environment to generate predicted values of photosynthetic and water‐use efficiency traits and test these against a unique dataset. Leaf gas‐exchange parameters and carbon isotope discrimination were analysed in relation to local climate across a continental network of study sites. Sun‐exposed leaves of 50 species at seven sites were measured in contrasting seasons. Values of χ predicted from growth temperature and vapour pressure deficit were closely correlated to ratios derived from C isotope (δ13C) measurements. Correlations were stronger in the growing season. Predicted values of photosynthetic traits, including carboxylation capacity (Vcmax), derived from δ13C, growth temperature and solar radiation, showed meaningful agreement with inferred values derived from gas‐exchange measurements. Between‐site differences in water‐use efficiency were, however, only weakly linked to the plant's growth environment and did not show seasonal variation. These results support the general hypothesis that many key parameters required by Earth system models are adaptive and predictable from plants' growth environments.

Rudge, Samuel L., and Kosov, Daniel S. (2019) Nonrenewal statistics in quantum transport from the perspective of first-passage and waiting time distributions. Physical Review B, 99 (11). 115426.
The waiting time distribution has, in recent years, proven to be a useful statistical tool for characterizing transport in nanoscale quantum transport. In particular, as opposed to moments of the distribution of transferred charge, which have historically been calculated in the long-time limit, waiting times are able to detect nonrenewal behavior in mesoscopic systems. They have failed, however, to correctly incorporate backtunneling events. Recently, a method has been developed that can describe unidirectional and bidirectional transport on an equal footing: the distribution of first-passage times. Rather than the time between successive electron tunnelings, the first passage refers to the first time the number of extra electrons in the drain reaches +1. Here, we demonstrate the differences between first-passage time statistics and waiting time statistics in transport scenarios where the waiting time either cannot correctly reproduce the higher-order current cumulants or cannot be calculated at all. To this end, we examine electron transport through a molecule coupled to two macroscopic metal electrodes. We model the molecule with strong electron-electron and electron-phonon interactions in three regimes: (i) sequential tunneling and cotunneling for a finite bias voltage through the Anderson model, (ii) sequential tunneling with no temperature gradient and a bias voltage through the Holstein model, and (iii) sequential tunneling at zero bias voltage and a temperature gradient through the Holstein model. We show that for each transport scenario, backtunneling events play a significant role; consequently, the waiting time statistics do not correctly predict the renewal and nonrenewal behavior, whereas the first-passage time distribution does.

Robertson, Sherryl G., and Glass, Beverley D. (2018) Stability of repackaged dabigatran etexilate capsules in dose administration AIDS. European Journal of Hospital Pharmacy, 25 (e2). e93-e97.
Objective: This study is aimed at assessing the stability of dabigatran etexilate (Pradaxa) capsules repackaged into a dose administration aid (DAA), in order to inform appropriate storage conditions that ensure quality. Although Pradaxa is used chronically by patients, and DAAs are known to improve adherence, removal of the capsules from their original packaging is not recommended by the manufacturer due to sensitivity to moisture. Methods: Pradaxa capsules containing dabigatran etexilate 110 mg were repackaged into a commercially available DAA and stored under ambient conditions (30°C±2°C and 75%±5% relative humidity) for periods of 14 and 28 days and in a domestic refrigerator for 28 days. The capsules were evaluated for changes in their physical appearance and weight. Content uniformity and the drug concentration during dissolution were determined using a validated high-performance liquid chromatography method. Results: Storage at ambient conditions for 14 and 28 days resulted in a percentage drug remaining of 92.5% and 71.6%, respectively, indicating a lack of compendial compliance (88.4%-111.8%) for the 28-day ambient sample. There was a statistically significant difference (p=0.015) in the dissolution behaviour of the 14-day samples, when compared with control capsules. In contrast, repackaged capsules stored in the refrigerator for 28 days had a drug content of 98.2% and dissolution was not significantly affected (p=0.132). Conclusion: This study has clearly demonstrated that if repackaging of Pradaxa capsules is required, storage under refrigerated conditions ensures quality for 28 days.

Konovalov, D.A., Domingos, J.A., White, R.D., and Jerry, D.R. (2018) Automatic scaling of fish images. In: Proceedings of the 2nd International Conference on Advances in Image Processing. pp. 48-53. From: ICAIP 18: 2nd International Conference on Advances in Image Processing, 16-18 June 2018, Chengdu, China.
In aquaculture breeding programs where large numbers of fish need to be rapidly phenotyped, the absolute physical dimensions of fish (in millimeters or inches) are often required to be extracted from electronic images in order to measure the size of the fish. While it is possible to infer the length of the fish in pixels, the absolute scale of the image (in pixels-per-millimeter or dots-per-inch) is largely unknown without a reference grid, or requires additional hardware, data collection and/or record-keeping management overheads. One cost and time effective solution is to capture the absolute scale by including a measuring ruler in the photographed scene and from which a computer program can automatically identify the scale of the photo and calculate fish morphometric measurements. To assist such workflow, this study developed an algorithm that automatically detects a ruler in a given image, and automatically extracts its scale as distance (in fractional number of pixels) between the ruler's graduation marks. The algorithm was applied to 445 publicly available images of barramundi or Asian seabass (Lates calcarifer), where a millimeter-graded ruler was included in each image. Convolutional Neural Network (CNN) was trained to segment the images into ruler, background, fish and label sections. Then the distance-extraction algorithm was applied to the ruler section of the images. The false-negative rate was less than 2%, where the ruler graduation distances could not be extracted in only 2-6 (out of 445) images even when the test images were rotated up to 90 degrees. The mean absolute relative error (MARE) of the inferred distances was 1-2%.

Konovalov, Dmitry A., Saleh, Alzayat, Domingos, Jose A., White, Ron D., and Jerry, Dean R. (2018) Estimating mass of harvested Asian seabass Lates calcarifer from images. World Journal of Engineering and Technology, 6 (3). pp. 15-23.
Total of 1072 Asian seabass or barramundi (Lates calcarifer) were harvested at two different locations in Queensland, Australia. Each fish was digitally photographed and weighed. A subsample of 200 images (100 from each location) were manually segmented to extract the fish-body area (S in cm2), excluding all fins. After scaling the segmented images to 1mm per pixel, the fish mass values (M in grams) were fitted by a single-factor model ( M=aS1.5 , a=0.1695 ) achieving the coefficient of determination (R2) and the Mean Absolute Relative Error (MARE) of R2=0.9819 and MARE=5.1% , respectively. A segmentation Convolutional Neural Network (CNN) was trained on the 200 hand-segmented images, and then applied to the rest of the available images. The CNN predicted fish-body areas were used to fit the mass-area estimation models: the single-factor model, M=aS1.5 , a=0.170 , R2=0.9819 , MARE=5.1% ; and the two-factor model, M=aSb , a=0.124 , b=0.155 , R2=0.9834 , MARE=4.5%

Grimbacher, Peter S., Edwards, Will, Liddell, Michael J., Nelson, Paul N., Nichols, Cassandra, Wardhaugh, Carl W., and Stork, Nigel E. (2018) Temporal variation in abundance of leaf litter beetles and ants in an Australian lowland tropical rainforest is driven by climate and litter fall. Biodiversity and Conservation, 27 (10). pp. 2625-2640.
Determining if the seasonality of leaf litter invertebrate populations in tropical rainforests is driven by climate or availability of litter, or both, is important to more accurately predict the vulnerability of litter invertebrates to climate change. Here we used two approaches to disentangle these effects. First, the influence of climatic seasonality was quantified by sampling a fixed volume of litter monthly over 4 years and counting extracted beetles and ants. Second, litter volume was experimentally manipulated (addition and exclusion) to test the influence of litter quantity independently of climatic variation. There were significant seasonal peaks for both beetle and ant abundance and these were positively correlated with rainfall, temperature and litter volume. As abundance was measured on a 'per litter volume' basis we conclude that there was a significant effect of climate on abundance. The litter manipulation experiment showed that beetle and ant abundance per litter volume were also influenced by litter volume, when it was low. We recognise that other factors such as litter structure or complexity may have affected temporal ant abundance. Beetle and ant abundance were depressed in litter exclusion plots but did not differ significantly between control and addition plots, suggesting a possible ceiling in the effect of litter volume on population sizes. We conclude that seasonality in climate and litter quantity are driving most temporal variation in insect abundance and that there may be some resilience among leaf litter insects to cope with higher temperatures. However, future responses by plants to increased climatic variability and higher CO2 concentrations may alter litter fall dynamics and thus temporal patterns in litter insect abundances.

Garland, Nathan Ashley (2018) Electron transport modeling in gas and liquid media for application in plasma medicine. PhD thesis, James Cook University.
Emerging plasma technologies, such as plasma medicine, rely on the transport of plasma species across gas-liquid interfaces to achieve their function. Recent studies have identified that, while poorly understood at present, electron transport through the interface is an important driver of plasma chemistry in plasma medicine. In order to understand this fundamental transport, so to facilitate understanding and future optimisation of plasma technologies, a modeling framework for electron transport simulations across gas-liquid interfaces has been developed. This modeling framework has been been applied to noble liquids, such as argon and xenon, and the first steps have been made towards application to a biomolecule system involving tetrahydrofuran. This research has extended previous approaches to electron fluid modeling in the gas phase to propose a fluid model for electron transport in gas and liquid media based on four moments of the Boltzmann kinetic equation. The model was benchmarked against kinetic solutions of electron transport to validate the applicability of the model to describe non-local electron transport phenomena in both gas and liquids, given that appropriate and accurate input data is available. To assess the impact of employing steady-state collision and closure input data in electron fluid models, non-equilibrium velocity distribution functions, computed via multi-term solution of the Boltzmann equation for benchmark calculations, were studied. The dependence of the proposed model's input transport data on the background medium density was examined in this research. By examining how electron momentum and energy transfer occurs due to collisions in gas and liquid extremes, an approximation method was proposed to generate input transport data at intermediate densities for which data is required, but not available, for modeling interfacial transport. The proposed approximation was benchmarked against analytic simple liquids and experimental data measured in cryogenic argon and xenon to verify the applicability of the proposed approach. Simulations of electron transport between gas and liquid argon, and vice versa, was performed by applying both the proposed fluid model and input data approximation method. Comparisons of the abilities of modeling methods to resolve realistic non-local transport were studied, and the stark differences between using electron-liquid transport data compared to simply scaling up electron-gas transport data were discussed. Application of this modeling framework to dual-phase simple liquid particle detector apparatus was demonstrated. Finally, application of the developed modeling framework was made to electron transport in tetrahydrofuran. To do so, a complete gas phase electron scattering cross section set was assembled and analysed using available experimental and theoretical data. Modifications of gas phase scattering to a simulated liquid phase were made using available experimental data. Comparison of streamer formation and propagation in both gaseous and simulated liquid tetrahydrofuran was studied to demonstrate applicability of the framework developed in this research to electron transport in biologically relevant soft-condensed matter.

Sankupellay, M., Middleby, K., Liddell, M.J., McKeown, A., and Westcott, D. (2018) Detection of flying-foxes using automated audio recorders. In: Proceedings of the 2018 Ecoacoustics Congress. p. 29. From: 2018 Ecoacoustics Congress, 24-28 June 2018, Brisbane, QLD, Australia.
Flying-foxes are little understood in Australia largely due to their extreme mobility. This mobility is particularly evident in the two species (spectacled and little red) found across the north of Australia, where huge numbers of animals will suddenly converge on a region and then leave a few weeks later. To improve management of these species we need to understand the movement and ecology of the animals and this is not straightforward as the camps are often remote and inaccessible. In this project we aimed to test the viability of using automated acoustic recorders for determining the presence of spectacled flying-foxes at camp locations. A Song Meter SM4 recorder was used to record flying-foxes in a number camps around South East QLD/Northern Rivers (black and grey-headed flying-foxes) and Cairns (spectacled flying-fox). A total of 35 hour of flying-foxes calls were recorded over a period of 8 weeks from August to October 2017. The recordings were processed using a Binary Winnow classifier and Hidden Markov Model in Kaleidoscope Software (Wildlife Acoustics). Tagged one-minute recordings were used to train the Hidden Markov Model in Kaleidoscope which was subsequently used in classifying the remaining recordings. Using this approach, we were able to quickly and easily detect the presence of flying-foxes in the acoustic recordings. In this way, ecologists can easily implement projects for long-term monitoring of flying-fox populations using remotely deployed acoustic recorders. It may also assist management agencies for urban planning in northern Australia. For future work, we will be investigate advanced machine learning algorithms coupled with flying-fox behavioural call patterns to attempt to distinguish the species of flying-fox from acoustic recordings.

Stokes, Peter W., Simonović, Ilija, Philippa, Bronson, Cocks, Daniel, Dujko, Sasa, and White, Ronald D. (2018) Third-order transport coefficients for localised and delocalised charged-particle transport. Scientific Reports, 8.
We derive third-order transport coefficients of skewness for a phase-space kinetic model that considers the processes of scattering collisions, trapping, detrapping and recombination losses. The resulting expression for the skewness tensor provides an extension to Fick’s law which is in turn applied to yield a corresponding generalised advection-diffusion-skewness equation. A physical interpretation of trap-induced skewness is presented and used to describe an observed negative skewness due to traps. A relationship between skewness, diffusion, mobility and temperature is formed by analogy with Einstein’s relation. Fractional transport is explored and its effects on the flux transport coefficients are also outlined.

Jaskowiak, Pablo A., Costa, Ivan G., and Campello, Ricardo J.G.B. (2018) Clustering of RNA-Seq samples: comparison study on cancer data. Methods, 132. pp. 42-49.
RNA-Seq is becoming the standard technology for large-scale gene expression level measurements, as it offers a number of advantages over microarrays. Standards for RNA-Seq data analysis are, however, in its infancy when compared to those of microarrays. Clustering, which is essential for understanding gene expression data, has been widely investigated w.r.t. microarrays. In what concerns the clustering of RNA-Seq data, however, a number of questions remain open, resulting in a lack of guidelines to practitioners. Here we evaluate computational steps relevant for clustering cancer samples via an empirical analysis of 15 mRNA-seq datasets. Our evaluation considers strategies regarding expression estimates, number of genes after non-specific filtering and data transformations. We evaluate the performance of four clustering algorithms and twelve distance measures, which are commonly used for gene expression analysis. Results support that clustering cancer samples based on a gene quantification should be preferred. The use of non-specific filtering leading to a small number of features (1,000) presents, in general, superior results. Data should be log-transformed previously to cluster analysis. Regarding the choice of clustering algorithms, Average-Linkage and k-medoids provide, in general, superior recoveries. Although specific cases can benefit from a careful selection of a distance measure, Symmetric Rank-Magnitude correlation provides consistent and sound results in different scenarios

Edwards, Will, Liddell, Michael J., Franks, Peter, Nichols, Cassandra, and Laurance, Susan G.W. (2018) Seasonal patterns in rainforest litterfall: detecting endogenous and environmental influences from long-term sampling. Austral Ecology, 43. pp. 225-235.
Tropical rainforests play an important role in the storage and cycling of global terrestrial carbon. In the carbon cycle, net primary productivity of forests is linked to soil respiration through the production and decomposition of forest litter. Climate seasonality appears to influence the production of litter although there is considerable variability within and across forests that makes accurate estimates challenging. We explored the effects of climate seasonality on litterfall dynamics in a lowland humid rainforest over a 7-year period from 2007 to 2013, including an El Ni~no/La Ni~na cycle in 2010/2011. Litterfall was sampled fortnightly in 24 traps of 0.50 m diameter within a 1-ha forest plot. Total mean litterfall was 10.48 Mt Carlton; high-sulfidation; epithermal; germanium; gallium; indium; critical elements; LA-ICP-MS; enargite; sphalerite 1.32 (Mt Carlton; high-sulfidation; epithermal; germanium; gallium; indium; critical elements; LA-ICP-MS; enargite; sphaleriteSD, dry weight) Mg ha -1 year -1 and seasonal in distribution. The different components of litterfall were divided into LLeaf (63.5%), LWood (27.7%) and LFF[flowers & fruit] (8.8%), which all demonstrated seasonal dynamics. Peak falls in LLeaf and LWood were highly predictable, coinciding with maximum daily temperatures and 1 and 2 months prior to maximum monthly rainfall. The El Ni~no/La Ni~na cycle coincided with elevated local winter temperatures and peak falls of LLeaf and LWood. Importantly, we establish how sampling length and generalized additive models eliminate the requirement for extensive within-site sampling when the intention is to describe dynamics in litterfall patterns. Further, a greater understanding of seasonal cycles in litterfall allows us to distinguish between endogenous controls and environmental factors, such as El Ni~no events, which may have significant impacts on biochemical cycles.

Gangur, Alex N., Seymour, Jamie E., Liddell, Michael J., Wilson, David, Smout, Michael J., and Northfield, Tobin D. (2018) When is overkill optimal? Tritrophic interactions reveal new insights into venom evolution. Theoretical Ecology, 11 (2). pp. 141-149.
Organisms embedded within food webs must balance arms races with their predators and prey. For venom users, venom may mediate each arms race, but the dynamical evolutionary changes in venom production in response to the two arms races are still poorly understood. Here, we use a simple model to evaluate the evolutionary response of a venomous consumer to the presence of an apex generalist predator and evolution of the consumer's prey. We find that introduction of the apex predator can weaken the arms race between the two lower trophic levels. In addition, when consumer prey capture and predator defense venoms functionally overlap, a reduced evolutionary response in the prey population can drive investment in venom used for prey capture going beyond what is optimal for subduing prey. These dynamics suggest that interactions with multiple trophic levels can substantially alter the venom complexity in predatory venomous animals and may explain the paradox of the overkill hypothesis.

Ali, Safaa H., Deacon, Glen B., Junk, Peter C., Hamidi, Shima, Wiecko, Michal, and Wang, Jun (2018) Lanthanoid pseudo‐Grignard reagents: a major untapped resource. Chemistry: a European journal, 24 (1). pp. 230-242.
Pseudo‐Grignard reagents PhLnI (Ln=Yb, Eu), readily prepared by the oxidative addition of iodobenzene to ytterbium or europium metal at −78 °C in tetrahydrofuran (THF) or 1,2‐dimethoxyethane (DME), react with a range of bulky N,N′‐bis(aryl)formamidines to generate an extensive series of LnII or more rarely LnIII complexes, namely [Eu(DippForm)I(thf)4]⋅thf (1), [{EuI2(dme)2}2] (2), [Eu(XylForm)I(dme)2]⋅0.5 dme (3 a), [Eu(XylForm)I(dme)(μ‐dme)]n (3 b), [{Eu(XylForm)I(μ‐OH)(thf)2}2] (4), [Yb(DippForm)I(thf)3]⋅thf (5 a), [Yb(DippForm)I2(thf)3]⋅2 thf (5 b), [{Yb(MesForm)I(thf)2}2] (6), [{Yb(XylForm)I(thf)2}2] (7 a), and [Yb(XylForm)2I(dme)]⋅dme (7 b) {(Form=ArNCHNAr; XylForm (Ar=2,6‐Me2C6H3), MesForm (Ar=2,4,6‐Me3C6H2), DippForm (Ar=2,6‐iPr2C6H3)}. Reaction of PhEuI and MesFormH in DME consistently gave 2, and reaction with XylFormH in THF gave 4. Europium complexes 1 and 3 a are seven‐coordinate divalent monomers, whilst 3 b is a seven‐coordinate dme‐bridged polymer. Complex 5 a of the smaller YbII is a six‐coordinate monomer, but the related 6 and 7 a are six‐coordinate iodide‐bridged dimers. 4 is a trivalent seven‐coordinate hydroxide‐bridged dimer, whereas complexes 5 b and 7 b are seven‐coordinate monomeric YbIII derivatives. A characteristic structural feature is that iodide ligands are cisoid to the formamidinate ligand. To illustrate the synthetic scope of the pseudo‐Grignard reagents, [Yb(Ph2pz)I(thf)4] (Ph2pz=3,5‐diphenylpyrazolate) was oxidised with 1,2‐diiodoethane to afford seven‐coordinate monomeric pyrazolato‐ytterbium(III) iodide [Yb(Ph2Pz)I2(thf)3] (8) in high yield, whilst metathesis between [Yb(Ph2pz)I(thf)4] and NaCp (Cp=C5H5) gave [Yb(C5H5)(Ph2pz)(thf)]n (9), a nine‐coordinate η5:η5‐Cp‐bridged coordination polymer. Reaction of the pseudo‐Grignard reagent MeYbI with KN(SiMe3)2 gave [K(dme)4][Yb{N(SiMe3)2}3] (10) with a charge‐separated three‐coordinate homoleptic [Yb{N(SiMe3)2}3]− anion, a complex that could be obtained in high yield by deliberate synthesis from YbI2 and KN(SiMe3)2 in DME.

Garland, Nathan, Boyle, Greg, Cocks, Daniel, and White, Ron (2018) Approximating the nonlinear density dependence of electron transport coefficients and scattering rates across the gas–liquid interface. Plasma Sources Science and Technology, 27.
This study reviews the neutral density dependence of electron transport in gases and liquids and develops a method to determine the nonlinear medium density dependence of electron transport coefficients and scattering rates required for modeling transport in the vicinity of gas–liquid interfaces. The method has its foundations in Blanc's law for gas-mixtures and adapts the theory of Garland et al (2017 Plasma Sources Sci. Technol. 26) to extract electron transport data across the gas–liquid transition region using known data from the gas and liquid phases only. The method is systematically benchmarked against multi-term Boltzmann equation solutions for Percus–Yevick model liquids. Application to atomic liquids highlights the utility and accuracy of the derived method.

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