A comparative study of density functional and density functional tight binding calculations of defects in graphene

The density functional tight binding approach (DFTB) is well adapted for the study of point and line defects in graphene based systems. After briefly reviewing the use of DFTB in this area, we present a comparative study of defect structures, energies and dynamics between DFTB results obtained using the dftb+ code, and density functional results using the localised Gaussian orbital code, AIMPRO. DFTB accurately reproduces structures and energies for a range of point defect structures such as vacancies and Stone-Wales defects in graphene, as well as various unfunctionalised and hydroxylated graphene sheet edges. Migration barriers for the vacancy and Stone-Wales defect formation barriers are accurately reproduced using a nudged elastic band approach. Finally we explore the potential for dynamic defect simulations using DFTB, taking as an example electron irradiation damage in graphene

Graphene edge structures: Folding, scrolling, tubing, rippling and twisting

Conventional three-dimensional crystal lattices are terminated by surfaces, which can demonstrate complex rebonding and rehybridisation, localised strain and dislocation formation. Two dimensional crystal lattices, of which graphene is the archetype, are terminated by lines. The additional available dimension at such interfaces opens up a range of new topological interface possibilities. We show that graphene sheet edges can adopt a range of topological distortions depending on their nature. Rehybridisation, local bond reordering, chemical functionalisation with bulky, charged, or multi-functional groups can lead to edge buckling to relieve strain, folding, rolling and even tube formation. We discuss the topological possibilities at a 2D graphene edge, and under what circumstances we expect different edge topologies to occur. Density functional calculations are used to explore in more depth different graphene edge types.Comment: Additional figure in published versio

Nomenclature of sp2 carbon nanoforms

Carbon’s versatile bonding has resulted in the discovery of a bewildering variety of nanoforms which urgently need a systematic and standard nomenclature [1]. Besides fullerenes, nanotubes and graphene, research teams around the globe now produce a plethora of carbon-based nanoforms such as ‘bamboo’ tubes, ‘herringbone’ and ‘bell’ structures. Each discovery duly gains a new, sometimes whimsical, name, often with its discoverer unaware that the same nanoform has already been reported several times but with different names (for example the nanoform in Fig. 1h is in different publications referred to as ‘bamboo’ [2], ‘herringbone-bamboo’ [3], ‘stacked-cups’ [4] and ‘stacked-cones’ [5]). In addition, a single name is often used to refer to completely different carbon nanoforms (for example, the ‘bamboo’ structure in [2] is notably different from ‘bamboo’ in [6]). The result is a confusing overabundance of names which makes literature searches and an objective comparison of results extremely difficult, if not impossible

The implications of climate change for the invasive tube worm Ficopomatus enigmaticus

Botany and Zoolog

Bromination of Graphene and Graphite

We present a density functional theory study of low density bromination of graphene and graphite, finding significantly different behaviour in these two materials. On graphene we find a new Br2 form where the molecule sits perpendicular to the graphene sheet with an extremely strong molecular dipole. The resultant Br+-Br- has an empty pz-orbital located in the graphene electronic pi-cloud. Bromination opens a small (86meV) band gap and strongly dopes the graphene. In contrast, in graphite we find Br2 is most stable parallel to the carbon layers with a slightly weaker associated charge transfer and no molecular dipole. We identify a minimum stable Br2 concentration in graphite, finding low density bromination to be endothermic. Graphene may be a useful substrate for stabilising normally unstable transient molecular states

Spatial organisation of proto-oncogenes in human haematopoietic progenitor cells

The eukaryotic cell nucleus is a highly organised organelle, with distinct specialised sub- compartments responsible for specific nuclear functions. Within the context of this functional framework, the genome is organised, allowing contact between specific genomic regions and sub-compartments. Previous work has shown that genes in both cis and trans can make specific contacts with each other. I hypothesise that such a preferred juxtaposition may impact the propensity for specific cancerinitiating chromosomal translocations to occur. In this thesis, I describe how I have extended and developed a ligation based proximity assay known as enriched 4C. I have coupled this technique with high throughput sequencing to determine genomic regions that spatially co-associate with the proto-oncogenes MLL, ABL1 and BCR. In addition to further developing the laboratory protocol, I have created bioinformatics tools used in the analysis of the sequencing data. I find that the association profiles of the three genes show strong correlation to the binding profile of RNA polymerase II and other active marks, suggesting that transcribed genes have a propensity to associate with other transcribed regions of the genome. Each gene also exhibits a unique repertoire of preferred associations with specific regions of the genome. Significantly, I find that the most frequent trans association of BCR is telomeric chromosome 9, encompassing its recurrent translocation partner gene ABL1. Interestingly, ABL1 is not at the maximum point of interaction. I use DNA-fluorescence in-situ hybridisation to validate the e4C association. My data supports a hypothesis that gene transcription has a direct role on genome organisation. I suggest that preferred co-associations of genes at transcription factories may promote the occurrence of specific chromosomal translocations

Supplementary report to the final report of the coral reef expert group: S4. Model to inform the design of a Reef Integrated Monitoring and Reporting Program

[Extract] This project developed a model to inform coral reef monitoring and management under the Reef 2050 Integrated Monitoring and Reporting Program (RIMReP) and the Reef 2050 Long-Term Sustainability Plan (Reef 2050 Plan). The model combines spatial statistical analyses with a mechanistic understanding of coral community dynamics. The purpose of the model is to analyse coral status and trend, and to guide the design of a coral monitoring program that most effectively captures these dynamics in space and time. This model uses per cent cover of hard corals and benthic composition as key indicators of reef state. Input variables include environmental data (e.g. temperature, salinity, sediment covers) and disturbance history (e.g. tropical cyclones, bleaching, water quality and outbreaks of the crown-of-thorns starfish). The model is calibrated against 20 years of in situ coral monitoring data and remotely sensed observations (1996-2015). A dual classification of all Great Barrier Reef (Reef) reefs was established based on (i) their benthic community composition and (ii) their coral cover trajectory over the 1996-2015 period, as a potential tool to stratify the future reef monitoring design. Both classifications, along with model outputs of coral cover, are available as a set of spatial layers (0.01 degree resolution).An accessible copy of this report is not yet available from this repository, please contact [email protected] for more information

Resources for Teaching Elementary General Music in Michigan Rural Public Schools

The purpose of this study was to determine what resources are available to general music teachers in distant and remote rural classrooms in Michigan. The areas of resources that were surveyed in this study included Human Resources (staffing, professional development), Contextual Resources (scheduling, facilities) and Instructional Resources (materials and equipment, curriculum), based on the National Association for Music Educators’ (NAfME) Opportunity-to-Learn Standards. Other data was gathered from teachers through open-ended questions that allowed teachers to describe the benefits, challenges, and greatest professional needs they experienced while teaching in a rural community. Specific research questions included: (a) What resources are available to teach elementary general music in rural public schools in the six areas of staffing and professional development; scheduling and facilities; and curriculum and materials and equipment? (b) How do the reported resources reflect the recommendations in the Opportunity-to-Learn Standards? The participants were public school elementary general music teachers who work in distant and remote rural locations in the state of Michigan. They were selected through a random sample of the schools listed on the Michigan Department of Education website in the distant and remote rural school categories. Participants were invited to complete an online survey that asked them to self-evaluate the quantity and quality of Human, Contextual and Instructional Resources at their school. Results from the survey were analyzed by category and revealed that while the data from this survey showed that more resources existed in rural schools than might be expected based on prior research, the types of resources (staffing, professional development, scheduling, facilities, materials and equipment, and curriculum) were available to varying degrees between schools. Music teachers in rural areas in Michigan reported little to no music-specific professional development offered by their school districts. While most school districts do not offer professional development specific to music education, teachers in rural schools feel isolated from the music education community because of the lack of music professional development. They also reported lacking music technology that their students could use to reinforce music concepts or that enable students to create and perform music. Finally, music teachers reported that old materials and equipment, and outdated curriculum were losing their value as resources, and that they had no budget to replace those resources. However, music teachers in rural areas also reported having abundant resources in their communities. The ability to know the students, their families, and the community members was reported as a valuable human resource and it ties in to the values of place-based theory—the theory that teachers thrive in communities that they connect with, and that their music programs thrive as well. While music teachers in all geographical locations lack various resources, it is important that we continue to study rural music education to continue to understand the challenges that arise from the lack of resources.Master of ArtsMusic EducationUniversity of Michiganhttps://deepblue.lib.umich.edu/bitstream/2027.42/137778/1/Anderson.CEE.Thesis.pdfDescription of Anderson.CEE.Thesis.pdf : Thesi

Comment on “Increase in specific heat and possible hindered rotation of interstitial C2 moleculesin neutron-irradiated graphite”

Iwata and Watanabe’s model for the observed low-temperature specific heat of neutron-irradiated graphite [T. Iwata and M. Watanabe, Phys. Rev. B 81, 014105 2010] assumes that self-interstitial atoms exist as clusters of nearly free C2 molecules. We suggest that their hypothesis is not supported by other experiments and theory, including our own calculations. Not only is it inconsistent with the long-known kinetics of interstitial prismatic dislocation loop formation, density-functional theory shows that the di-interstitial is covalently bonded to the host crystal. In such calculations no prior assumptions are made about the nature of the bonding, covalent or otherwise

Adatoms and nanoengineering of carbon

We present a new and general mechanism for inter-conversion of carbon structures via a catalytic exchange process, which operates under conditions of Frenkel pair generation. The mechanism typically lowers reaction barriers by a factor of four compared to equivilent uncatalysed reactions. We examine the relevance of this mechanism for fullerene growth, carbon onions and nanotubes, and dislocations in irradiated graphite.Comment: 3 Figures, 5 Page letter accepted for publication in Chemical Physics Letter