The modelling of feedback in star formation simulations

This document is the Accepted Manuscript version of the following article: James E. Dale, ‘The modelling of feedback in star formation simulations’, New Astronomy Reviews, Vol. 68, pp. 1-33, October 2015. This article is distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License (http://creativecommons.org/licenses/by-nc-nd/4.0/ ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way. The final, published version is available online at doi:https://doi.org/10.1016/j.newar.2015.06.001. © 2015 Elsevier B.V. All rights reserved.I review the current state of numerical simulations of stellar feedback in the context of star formation at scales ranging from the formation of individual stars to models of galaxy formation including cosmic reionisation. I survey the wealth of algorithms developed recently to solve the radiative transfer problem and to simulate stellar winds, supernovae and protostellar jets. I discuss the results of these simulations with regard to star formation in molecular clouds, the interaction of different feedback mechanisms with each other and with magnetic fields, and in the wider context of galactic- and cosmological-scale simulations.Peer reviewe

NMR DIFFUSION MEASUREMENTS OF COMPARTMENTALIZED AND MULTICOMPONENT BIOLOGICAL SYSTEMS: Studies of Tropoelastin, the Self Association of N Methylacetamide, and q-Space Analysis of Real and Model Cell Suspensions

Molecular diffusion is an inherent feature of all fluid systems. The processes and interactions that characterize these systems are in some way dependent upon the mobility of the component molecules. Pulsed field-gradient spin-echo nuclear magnetic resonance (PGSE NMR) is a powerful tool for the study of molecular diffusion; for heterogeneous systems, such as those typically found in biology, this technique is unsurpassed in the diversity of systems that yield to its probing. The aim of the work presented in this thesis was to use an integrated NMR-based approach, in conjunction with computer modeling, for the study of molecular diffusion in compartmentalized and multicomponent biological systems. Erythrocyte suspensions provided an ideal experimental system for the study of compartmentalized diffusion in cells. Water exchanges rapidly between the intra- and extracellular regions and, as the major constituent of the cell, provides a strong and predominant proton NMR signal. In addition, the cells are known to align in the strong static magnetic field of the spectrometer. As a consequence of these two properties, the signal intensity from a suitably designed series of PGSE NMR experiments exhibits a series of maxima and minima when graphed as a function of the magnitude of the spatial wave number vector q. The apparently periodic phenomenon is mathematically analogous to optical diffraction and interference and is referred to here as diffusion-coherence. It is the characterization of this phenomenon, with the aid of computer-based models, which was the focus of a major section of the work described herein. Two quite distinct molecular systems formed the basis of the work in which I investigated diffusion in multicomponent systems. Both systems involved molecules that undergo self-association such that at equilibrium a population distribution of different oligomeric species is present. The first of these was tropoelastin, the monomeric subunit of elastin, which under certain conditions aggregates to form a coacervate. The second system was N-methylacetamide (NMA) which also undergoes extensive self-association. NMA oligomers have previously been studied as peptide analogues due to the presence in the monomer of a peptide linkage. In this work the aim was to use PGSE NMR diffusion measurements, in a manner that is in many ways analogous to analytical ultracentrifugation, to obtain estimates of hydrodynamic and thermodynamic parameters. Computer modeling was also used extensively in this section of work for the interpretation of the experimental data

NMR DIFFUSION MEASUREMENTS OF COMPARTMENTALIZED AND MULTICOMPONENT BIOLOGICAL SYSTEMS: Studies of Tropoelastin, the Self Association of N Methylacetamide, and q-Space Analysis of Real and Model Cell Suspensions

Molecular diffusion is an inherent feature of all fluid systems. The processes and interactions that characterize these systems are in some way dependent upon the mobility of the component molecules. Pulsed field-gradient spin-echo nuclear magnetic resonance (PGSE NMR) is a powerful tool for the study of molecular diffusion; for heterogeneous systems, such as those typically found in biology, this technique is unsurpassed in the diversity of systems that yield to its probing. The aim of the work presented in this thesis was to use an integrated NMR-based approach, in conjunction with computer modeling, for the study of molecular diffusion in compartmentalized and multicomponent biological systems. Erythrocyte suspensions provided an ideal experimental system for the study of compartmentalized diffusion in cells. Water exchanges rapidly between the intra- and extracellular regions and, as the major constituent of the cell, provides a strong and predominant proton NMR signal. In addition, the cells are known to align in the strong static magnetic field of the spectrometer. As a consequence of these two properties, the signal intensity from a suitably designed series of PGSE NMR experiments exhibits a series of maxima and minima when graphed as a function of the magnitude of the spatial wave number vector q. The apparently periodic phenomenon is mathematically analogous to optical diffraction and interference and is referred to here as diffusion-coherence. It is the characterization of this phenomenon, with the aid of computer-based models, which was the focus of a major section of the work described herein. Two quite distinct molecular systems formed the basis of the work in which I investigated diffusion in multicomponent systems. Both systems involved molecules that undergo self-association such that at equilibrium a population distribution of different oligomeric species is present. The first of these was tropoelastin, the monomeric subunit of elastin, which under certain conditions aggregates to form a coacervate. The second system was N-methylacetamide (NMA) which also undergoes extensive self-association. NMA oligomers have previously been studied as peptide analogues due to the presence in the monomer of a peptide linkage. In this work the aim was to use PGSE NMR diffusion measurements, in a manner that is in many ways analogous to analytical ultracentrifugation, to obtain estimates of hydrodynamic and thermodynamic parameters. Computer modeling was also used extensively in this section of work for the interpretation of the experimental data

Economic viability of implementing an infrastructure for recycling bedding sand from a free-stall facility for dairy cows.

This study proposes to examine the economic viability of implementing the necessary infrastructure for the recycling of bedding sand from a free-stall facility in a milk production system in southern Minas Gerais, Brazil. In specific terms, the total production cost (TC), total operating cost (TOC) and effective operating cost (EOC) of a cubic meter of recycled sand were estimated in order to estimate the total sand consumption for the free-stall system and per bed year-1 as well as the equilibrium point of the amount of recycled sand, in cubic meters. The experiment was carried out on a farm located in the south of Minas Gerais from January 2016 to December 2017. Three scenarios were analyzed by the tree-point estimation method (MOP - most likely, optimistic, and pessimistic). Utilization of 85%, 95% and 75% of the recycled sand was considered for scenarios 1, 2 and 3, respectively. In all of them, the value charged per cubic meter of sand by a supplier close to the farm was considered. Monte Carlo simulation was also carried out with hurdle rates (HR) of up to 90%. Under the studied conditions, sand recycling showed to be economically viable in all scenarios, with positive net present values (NPV), internal rates of return above the HR, simple and discounted payback below the 10-year horizon, and satisfactory cost benefit-1 ratios (greater than 1). The EOC of one cubic meter of recycled sand was estimated at R$5.04, R$4.51 and R$5.72 for scenarios 1, 2 and 3, respectively, whereas the average TC, considering all scenarios, was R$6.84 (+0.81), which is less than the acquisition price of R$28.57 at the sand extraction site. The TC was R$37,219.51 and R$34,637.74 for the scenarios with HR of 8.50 and 6.99$22,572.08 in all analyzed scenarios. The estimated total annual sand consumption by the free-stall system was 526.44 m³, with an estimated average of 1.23 m³ (+0.28) bed-1 year-1. All Monte Carlo simulation models showed positive NPV as well as HR of up to 90%, which reflect a high probability of positive NPV

Contrasting evolutionary history, anthropogenic declines and genetic contact in the northern and southern white rhinoceros (Ceratotherium simum)

The white rhinoceros (Ceratotherium simum) has a discontinuous African distribution, which is limited by the extent of sub-Saharan grasslands. The southern population (SWR) declined to its lowest number around the turn of the nineteenth century, but recovered to become the world's most numerous rhinoceros. In contrast, the northern population (NWR) was common during much of the twentieth century, declining rapidly since the 1970s, and now only two post-reproductive individuals remain. Despite this species's conservation status, it lacks a genetic assessment of its demographic history. We therefore sampled 232 individuals from extant and museum sources and analysed ten microsatellite loci and the mtDNA control region. Both marker types reliably partitioned the species into SWR and NWR, with moderate nuclear genetic diversity and only three mtDNA haplotypes for the species, including historical samples. We detected ancient interglacial demographic declines in both populations. Both populations may also have been affected by recent declines associated with the colonial expansion for the SWR, and with the much earlier Bantu migrations for the NWR. Finally, we detected post-divergence secondary contact between NWR and SWR, possibly occurring as recently as the last glacial maximum. These results suggest the species was subjected to regular periods of fragmentation and low genetic diversity, which may have been replenished upon secondary contact during glacial periods. The species's current situation thus reflects prehistoric declines that were exacerbated by anthropogenic pressure associated with the rise of late Holocene technological advancement in Africa. Importantly, secondary contact suggests a potentially positive outcome for a hybrid rescue conservation strategy, although further genome-wide data are desirable to corroborate these results

Contrasting evolutionary history, anthropogenic declines and genetic contact in the northern and southern white rhinoceros (Ceratotherium simum)

The white rhinoceros (Ceratotherium simum) has a discontinuous African distribution, which is limited by the extent of sub-Saharan grasslands. The southern population (SWR) declined to its lowest number around the turn of the nineteenth century, but recovered to become the world's most numerous rhinoceros. In contrast, the northern population (NWR) was common during much of the twentieth century, declining rapidly since the 1970s, and now only two post-reproductive individuals remain. Despite this species's conservation status, it lacks a genetic assessment of its demographic history. We therefore sampled 232 individuals from extant and museum sources and analysed ten microsatellite loci and the mtDNA control region. Both marker types reliably partitioned the species into SWR and NWR, with moderate nuclear genetic diversity and only three mtDNA haplotypes for the species, including historical samples. We detected ancient interglacial demographic declines in both populations. Both populations may also have been affected by recent declines associated with the colonial expansion for the SWR, and with the much earlier Bantu migrations for the NWR. Finally, we detected post-divergence secondary contact between NWR and SWR, possibly occurring as recently as the last glacial maximum. These results suggest the species was subjected to regular periods of fragmentation and low genetic diversity, which may have been replenished upon secondary contact during glacial periods. The species's current situation thus reflects prehistoric declines that were exacerbated by anthropogenic pressure associated with the rise of late Holocene technological advancement in Africa. Importantly, secondary contact suggests a potentially positive outcome for a hybrid rescue conservation strategy, although further genome-wide data are desirable to corroborate these results

Biodiversity of the Coccidia (Apicomplexa: Conoidasida) in Vertebrates: What We Know, What We Do Not Know, and What Needs to Be Done

Over the last two decades my colleagues and I have assembled the literature on a good percentage of most of the coccidians (Conoidasida) known, to date, to parasitise: Amphibia, four major lineages of Reptilia (Amphisbaenia, Chelonia, Crocodylia, Serpentes), and seven major orders in the Mammalia (Carnivora, Chiroptera, Lagomorpha, Insectivora, Marsupialia, Primates, Scandentia). These vertebrates, combined, comprise about 15,225 species; only about 899 (5.8%) of them have been surveyed for coccidia and 1,946 apicomplexan valid species names or other forms are recorded in the literature. Based on these compilations and other factors, I extrapolated that there yet may be an additional 31,381 new apicomplexans still to be discovered in just these 12 vertebrate groups. Extending the concept to all of the other extant vertebrates on Earth; i.e. lizards (6,300 spp.), rodents plus 12 minor orders of mammals (3,180 spp.), birds (10,000 spp.), and fishes (33,000 spp.) and, conservatively assuming only two unique apicomplexan species per each vertebrate host species, I extrapolate and extend my prediction that we may eventually find 135,000 new apicomplexans that still need discovery and to be described in and from those vertebrates that have not yet been examined for them! Even doubling that number is a significant underestimation in my opinion

Formation and feedback processes of massive stars in clusters

Many uncertainties remain as to how the most massive stars are formed and how they interact with their environment via radiative and mechanical processes. This feedback may affect future generations of star formation -- triggering it by compressing gas, or hindering it by dispersing reservoirs. These scenarios can be simulated by solving the equations of hydrodynamics and radiative transfer. However, the latter is usually simplified due to its computational expense, despite its importance in determining the dynamics. In this thesis, I describe how I increased the efficiency of the radiation hydrodynamics code, TORUS, which uses a Monte Carlo approach to solving the radiative transfer. Tens of millions of energy packets are propagated through a domain split over hundreds of processors running in parallel with Message Passing Interface (MPI). By re-examining and improving communication algorithms, I lowered the radiation run time by about a factor of ten, making it tractable to run three-dimensional simulations of massive star feedback in clusters. This includes both the stellar and diffuse radiation fields, with multiple atomic species and silicate dust grains. The full ionization states and temperatures can then be fed in to produce self-consistent synthetic observations. I applied this to clouds of 1000 and 10,000 solar masses with surface density 0.01 g/cm^2, containing a 34 solar mass star, with photoionization and radiation pressure feedback. Photoionization is efficient at shaping and dispersing clouds. The expanding ionization front forms dense, spherical knots with pillars pointing away from the emitting star. These resemble the Pillars of Creation in the Eagle Nebula, and the proplyds observed in the Orion Nebula. In the lower-mass model, almost all material is removed from the (15.5 pc)^3 grid within 1.6 Myr; the higher mass cloud is somewhat more resistant, with 25 per cent remaining inside (32.3 pc)^3 after 4.3 Myr. Radiation pressure has a negligible effect, but will be more important for denser clouds or higher luminosities.Science and Technology Facilities Council (STFC

Integrating GIS approaches with geographic profiling as a novel conservation tool

PhDGeographic profiling (GP) was originally developed to solve the problem of information overload when dealing with cases of serial crime. In criminology, the model uses spatial data relating to the locations of connected crimes to prioritise the search for the criminal’s anchor point (usually a home or workplace), and is extremely successful in this field. Previous work has shown how the same approach can be adapted to biological data, but to date the model has assumed a spatially homogenous landscape, and has made no attempt to integrate more complex spatial information (eg, altitude, land use). It is this issue that I address here. In addition, I show for the first time how the model can be applied to conservation data and – taking the model back to its origins in criminology – to wildlife crime. In Chapter 2, I use the Dirichlet Process Mixture (DPM) model of geographic profiling to locate sleep trees for tarsiers in dense jungle in Indonesia, using as input the locations at which calls were recorded, demonstrating how the model can be applied to locating the nests, dens or roosts of other elusive animals and potentially improving estimates of population size, with important implications for management of both species and habitats. In Chapter 3, I show how spatial information in the form of citizen science could be used to improve a study of invasive mink in the Hebrides. In Chapter 4, I turn to the issue of ‘commuter crime’ in a study of poaching in Savé Valley Conservancy (SVC) in Zimbabwe, in which although poaching occurs inside SVC the majority of poachers live outside, showing how the model can be adjusted to reflect a simple binary classification of the landscape (inside or outside SVC). Finally, in Chapter 5, I combine more complex land use information (estimates of farm density) with the GP model to improve predictions of human-wildlife conflict.National Environment Research Council and Queen Mary University of London

2017 Conference Abstracts: Annual Undergraduate Research Conference at the Interface of Biology and Mathematics

Schedule and abstract book for the Ninth Annual Undergraduate Research Conference at the Interface of Biology and Mathematics Date: November 11-12, 2017Location: UT Conference Center, KnoxvillePlenary Speaker: Kiona Ogle, The School of Informatics, Computing, and Cyber Systems, Northern Arizona Univ.Featured Speaker: Katherine J. Evans, Group Leader, Computational Earth Sciences, ORN