Shingle 2.0: generalising self-consistent and automated domain discretisation for multi-scale geophysical models

The approaches taken to describe and develop spatial discretisations of the domains required for geophysical simulation models are commonly ad hoc, model or application specific and under-documented. This is particularly acute for simulation models that are flexible in their use of multi-scale, anisotropic, fully unstructured meshes where a relatively large number of heterogeneous parameters are required to constrain their full description. As a consequence, it can be difficult to reproduce simulations, ensure a provenance in model data handling and initialisation, and a challenge to conduct model intercomparisons rigorously. This paper takes a novel approach to spatial discretisation, considering it much like a numerical simulation model problem of its own. It introduces a generalised, extensible, self-documenting approach to carefully describe, and necessarily fully, the constraints over the heterogeneous parameter space that determine how a domain is spatially discretised. This additionally provides a method to accurately record these constraints, using high-level natural language based abstractions, that enables full accounts of provenance, sharing and distribution. Together with this description, a generalised consistent approach to unstructured mesh generation for geophysical models is developed, that is automated, robust and repeatable, quick-to-draft, rigorously verified and consistent to the source data throughout. This interprets the description above to execute a self-consistent spatial discretisation process, which is automatically validated to expected discrete characteristics and metrics.Comment: 18 pages, 10 figures, 1 table. Submitted for publication and under revie

Dividing population genetic distance data with the software Partitioning Optimization with Restricted Growth Strings (PORGS): an application for Chinook salmon (Oncorhynchus tshawytscha), Vancouver Island, British Columbia

A new method of finding the optimal group membership and number of groupings to partition population genetic distance data is presented. The software program Partitioning Optimization with Restricted Growth Strings (PORGS), visits all possible set partitions and deems acceptable partitions to be those that reduce mean intracluster distance. The optimal number of groups is determined with the gap statistic which compares PORGS results with a reference distribution. The PORGS method was validated by a simulated data set with a known distribution. For efficiency, where values of n were larger, restricted growth strings (RGS) were used to bipartition populations during a nested search (bi-PORGS). Bi-PORGS was applied to a set of genetic data from 18 Chinook salmon (Oncorhynchus tshawytscha) populations from the west coast of Vancouver Island. The optimal grouping of these populations corresponded to four geographic locations: 1) Quatsino Sound, 2) Nootka Sound, 3) Clayoquot +Barkley sounds, and 4) southwest Vancouver Island. However, assignment of populations to groups did not strictly reflect the geographical divisions; fish of Barkley Sound origin that had strayed into the Gold River and close genetic similarity between transferred and donor populations meant groupings crossed geographic boundaries. Overall, stock structure determined by this partitioning method was similar to that determined by the unweighted pair-group method with arithmetic averages (UPGMA), an agglomerative clustering algorithm

Numerical solution of perturbed Kepler problem using a split operator technique

An efficient geometric integrator is proposed for solving the perturbed Kepler motion. This method is stable and accurate over long integration time, which makes it appropriate for treating problems in astrophysics, like solar system simulations, and atomic and molecular physics, like classical simulations of highly excited atoms in external fields. The key idea is to decompose the hamiltonian in solvable parts and propagate the system according to each term. Two case studies, the Kepler atom in an uniform field and in a monochromatic field, are presented and the errors are analyzed.Comment: 17 pages, 5 figures, submitted to the Journal of Computational Physic

The impact of detoxification costs and predation risk on foraging : implications for mimicry dynamics

This work was supported by the European Research Council (Advanced Grant 250209 to Alasdair Houston), a Natural Environment Research Council Independent Research Fellowship (NE/L011921/1) awarded to A.D.H., a BBSRC-NERC project grant (BB/G00188X/1) awarded to J.S., C.R. and G.D.R. and a faculty fellowship awarded to C.G.H. (Medical Sciences, Newcastle University) with strategic support funding from the Wellcome Trust.Prey often evolve defences to deter predators, such as noxious chemicals including toxins. Toxic species often advertise their defence to potential predators by distinctive sensory signals. Predators learn to associate toxicity with the signals of these so-called aposematic prey, and may avoid them in future. In turn, this selects for mildly toxic prey to mimic the appearance of more toxic prey. Empirical evidence shows that mimicry could be either beneficial (‘Mullerian’) or detrimental (‘quasi-Batesian’) to the highly toxic prey, but the factors determining which are unknown. Here, we use state-dependent models to explore how tri-trophic interactions could influence the evolution of prey defences. We consider how predation risk affects predators’ optimal foraging strategies on aposematic prey, and explore the resultant impact this has on mimicry dynamics between unequally defended species. In addition, we also investigate how the potential energetic cost of metabolising a toxin can alter the benefits to eating toxic prey and thus impact on predators’ foraging decisions. Our model predicts that both how predators perceive their own predation risk, and the cost of detoxification, can have significant, sometimes counterintuitive, effects on the foraging decisions of predators. For example, in some conditions predators should: (i) avoid prey they know to be undefended, (ii) eat more mildly toxic prey as detoxification costs increase, (iii) increase their intake of highly toxic prey as the abundance of undefended prey increases. These effects mean that the relationship between a mimic and its model can qualitatively depend on the density of alternative prey and the cost of metabolising toxins. In addition, these effects are mediated by the predators’ own predation risk, which demonstrates that, higher trophic levels than previously considered can have fundamental impacts on interactions among aposematic prey species.Publisher PDFPeer reviewe

Altered Cerebellar Short-Term Plasticity but No Change in Postsynaptic AMPA-Type Glutamate Receptors in a Mouse Model of Juvenile Batten Disease

Juvenile Batten disease is the most common progressive neurodegenerative disorder of childhood. It is associated with mutations in the CLN3 gene, causing loss of function of CLN3 protein and degeneration of cerebellar and retinal neurons. It has been proposed that changes in granule cell AMPA-type glutamate receptors (AMPARs) contribute to the cerebellar dysfunction. In this study we compared AMPAR properties and synaptic transmission in cerebellar granule cells from wild-type and Cln3 knockout mice. In Cln3Δex1–6 cells the amplitude of AMPA-evoked whole-cell currents was unchanged. Similarly, we found no change in the amplitude, kinetics, or rectification of synaptic currents evoked by individual quanta, or in their underlying single-channel conductance. We found no change in cerebellar expression of GluA2 or GluA4 protein. By contrast, we observed a reduced number of quantal events following mossy-fiber stimulation in Sr2+, altered short-term plasticity in conditions of reduced extracellular Ca2+, and reduced mossy fiber vesicle number. Thus, while our results suggest early presynaptic changes in the Cln3Δex1–6 mouse model of juvenile Batten disease, they reveal no evidence for altered postsynaptic AMPARs

Acid-sensing ion channel 1a drives AMPA receptor plasticity following ischemia and acidosis in hippocampal CA1 neurons

The CA1 region of the hippocampus is particularly vulnerable to ischemic damage. While NMDA receptors play a major role in excitotoxicity, it is thought to be exacerbated in this region by two forms of post-ischemic AMPA receptor (AMPAR) plasticity - namely, anoxic long-term potentiation (a-LTP), and a delayed increase in the prevalence of Ca2+ -permeable GluA2-lacking AMPARs (CP-AMPARs). The acid-sensing ion channel 1a (ASIC1a) which is expressed in CA1 pyramidal neurons, is also known to contribute to post-ischemic neuronal death and to physiologically induced LTP. This raises the question - does ASIC1a activation drive the post-ischemic forms of AMPAR plasticity in CA1 pyramidal neurons? We have tested this by examining organotypic hippocampal slice cultures (OHSCs) exposed to oxygen glucose deprivation (OGD), and dissociated cultures of hippocampal pyramidal neurons (HPN) exposed to low pH (acidosis). We find that both a-LTP and the delayed increase in the prevalence of CP-AMPARs are dependent on ASIC1a activation during ischemia. Indeed, acidosis alone is sufficient to induce the increase in CP-AMPARs. We also find that inhibition of ASIC1a channels circumvents any potential neuroprotective benefit arising from block of CP-AMPARs. By demonstrating that ASIC1a activation contributes to post-ischemic AMPAR plasticity, our results identify a functional interaction between acidotoxicity and excitotoxicity in hippocampal CA1 cells, and provide insight into the role of ASIC1a and CP-AMPARs as potential drug targets for neuroprotection. We thus propose that ASIC1a activation can drive certain forms of CP-AMPAR plasticity, and that inhibiting ASIC1a affords neuroprotection

An Enhanced Nonlinear Critical Gradient for Electron Turbulent Transport due to Reversed Magnetic Shear

The first nonlinear gyrokinetic simulations of electron internal transport barriers (e-ITBs) in the National Spherical Torus Experiment show that reversed magnetic shear can suppress thermal transport by increasing the nonlinear critical gradient for electron-temperature-gradient-driven turbulence to three times its linear critical value. An interesting feature of this turbulence is nonlinearly driven off-midplane radial streamers. This work reinforces the experimental observation that magnetic shear is likely an effective way of triggering and sustaining e-ITBs in magnetic fusion devices.Comment: 4 pages, 5 figure

An Enhanced Nonlinear Critical Gradient for Electron Turbulent Transport due to Reversed Magnetic Shear

The first nonlinear gyrokinetic simulations of electron internal transport barriers (e-ITBs) in the National Spherical Torus Experiment show that reversed magnetic shear can suppress thermal transport by increasing the nonlinear critical gradient for electron-temperature-gradient-driven turbulence to three times its linear critical value. An interesting feature of this turbulence is nonlinearly driven off-midplane radial streamers. This work reinforces the experimental observation that magnetic shear is likely an effective way of triggering and sustaining e-ITBs in magnetic fusion devices.Comment: 4 pages, 5 figure

Molecular mechanisms contributing to TARP regulation of channel conductance and polyamine block of calcium-permeable AMPA receptors.

Many properties of fast synaptic transmission in the brain are influenced by transmembrane AMPAR regulatory proteins (TARPs) that modulate the pharmacology and gating of AMPA-type glutamate receptors (AMPARs). Although much is known about TARP influence on AMPAR pharmacology and kinetics through their modulation of the extracellular ligand-binding domain (LBD), less is known about their regulation of the ion channel region. TARP-induced modifications in AMPAR channel behavior include increased single-channel conductance and weakened block of calcium-permeable AMPARs (CP-AMPARs) by endogenous intracellular polyamines. To investigate how TARPs modify ion flux and channel block, we examined the action of γ-2 (stargazin) on GluA1 and GluA4 CP-AMPARs. First, we compared the permeation of organic cations of different sizes. We found that γ-2 increased the permeability of several cations but not the estimated AMPAR pore size, suggesting that TARP-induced relief of polyamine block does not reflect altered pore diameter. Second, to determine whether residues in the TARP intracellular C-tail regulate polyamine block and channel conductance, we examined various γ-2 C-tail mutants. We identified the membrane proximal region of the C terminus as crucial for full TARP-attenuation of polyamine block, whereas complete deletion of the C-tail markedly enhanced the TARP-induced increase in channel conductance; thus, the TARP C-tail influences ion permeation. Third, we identified a site in the pore-lining region of the AMPAR, close to its Q/R site, that is crucial in determining the TARP-induced changes in single-channel conductance. This conserved residue represents a site of TARP action, independent of the AMPAR LBD