Towards a lightweight generic computational grid framework for biological research

Background: An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations – a characteristic of the emerging field of systems biology. Results: In this paper we present a lightweight generic framework for combining disparate computational resources at multiple sites (ranging from local computers and clusters to established national Grid services). A detailed guide describing how to set up the framework is available from the following URL: http://igrid-ext.cryst.bbk.ac.uk/portal_guide/. Conclusion: This approach is particularly (but not exclusively) appropriate for large-scale biology projects with multiple collaborators working at different national or international sites. The framework is relatively easy to set up, hides the complexity of Grid middleware from the user, and provides access to resources through a single, uniform interface. It has been developed as part of the European ImmunoGrid project

Test of the proximity theorem for deformed nuclei

We compare a proximity-type potential for two interacting nuclei with the double-folding method. Both spherical and deformed systems are considered. Special "orientation windows" are found for two deformed nuclei giving rise to nuclear cohesion. If the same nucleon-nucleon interaction is utilized, the proximity and the double-folding potentials agree fairly well for a spherical + deformed system. However, deviations are found in the case of two deformed nuclei

Magnetic Wreaths and Cycles in Convective Dynamos

Solar-type stars exhibit a rich variety of magnetic activity. Seeking to explore the convective origins of this activity, we have carried out a series of global 3D magnetohydrodynamic (MHD) simulations with the anelastic spherical harmonic (ASH) code. Here we report on the dynamo mechanisms achieved as the effects of artificial diffusion are systematically decreased. The simulations are carried out at a nominal rotation rate of three times the solar value (3$\Omega_\odot$), but similar dynamics may also apply to the Sun. Our previous simulations demonstrated that convective dynamos can build persistent toroidal flux structures (magnetic wreaths) in the midst of a turbulent convection zone and that high rotation rates promote the cyclic reversal of these wreaths. Here we demonstrate that magnetic cycles can also be achieved by reducing the diffusion, thus increasing the Reynolds and magnetic Reynolds numbers. In these more turbulent models, diffusive processes no longer play a significant role in the key dynamical balances that establish and maintain the differential rotation and magnetic wreaths. Magnetic reversals are attributed to an imbalance in the poloidal magnetic induction by convective motions that is stabilized at higher diffusion levels. Additionally, the enhanced levels of turbulence lead to greater intermittency in the toroidal magnetic wreaths, promoting the generation of buoyant magnetic loops that rise from the deep interior to the upper regions of our simulated domain. The implications of such turbulence-induced magnetic buoyancy for solar and stellar flux emergence are also discussed.Comment: 21 pages, 16 figures, accepted for publication in Ap

Taxing Retirement Income: Nonqualified Annuities and Distributions from Qualified Accounts

This paper explores the current tax treatment of non-qualified immediate annuities and distributions from tax-qualified retirement plans in the United States. First, we describe how immediate annuities held outside retirement accounts are taxed. We conclude that the current income tax treatment of annuities does not substantially alter the incentive to purchase an annuity rather than a taxable bond. We nevertheless find differences across different individuals in the effective tax burden on annuity contracts. Second, we examine an alternative method of taxing annuities that would avoid changing the fraction of the annuity payment that is included in taxable income as the annuitant ages, but would still raise the same expected present discounted value of revenues as the current income tax rule. We find that a shift to a constant inclusion ratio increases the utility of annuitants, and that this increase is greater for more risk averse individuals. Third, we examine how payouts from qualified accounts are taxed, focusing on both annuity payouts and minimum distribution requirements that constrain the feasible time path of nonannuitized payouts. We describe briefly the origins and workings of the minimum distribution rules and we also provide evidence on the fraction of retirement assets potentially affected by these rules.

Cautioning the move from morphology to molecules in the taxonomy of Metazoa: Comments on Lawley et al. (PeerJ 2021;9, e11954) and a plea for considered integration

This paper serves as a commentary on a recently published paper by Lawley et al. (PeerJ 2021;9, e11954). We caution the adoption of practices in the taxonomy of Scyphozoa by Lawley et al. on the basis that they may lead to taxonomic splits and parallel taxonomies in the face of a concerted push towards integrative taxonomy