Discovering and Understanding High Performance Materials using Density Functional Theory: Quantum Mechanical Simulations and the Consequences of Symmetry

There are two primary ways that atomic level modeling data is used: materials prediction and understanding materials properties. This dissertation work encom- passes two studies, each of which explore one application. Both studies rely on the highly successful density functional theory (DFT) formalism but differ in that two different implementations of DFT are used on two different high performance materials. The first study on bulk magnesium (Mg) metal alloys explores materials prediction and relies on VASP, a commercially maintained plane-wave DFT code which has been used extensively to successfully study a wide range of materials. [1] The approach used in this first study is to ‘experiment’ within computational quantum mechanical simulations to improve the elastic properties of bulk Mg by altering its HCP lattice structure. We systematically study the influence of adding lithium (Li) as an alloy for two reasons: to maintain the lightweight benefits of Mg, and Li naturally occurs in a body centered cubic (BCC) crystal structure. The hypothesis is that an alloy with a more symmetric crystal structure will show im- proved properties, however we do not place any symmetry restrictions on the results of the structure search. We find that the addition of Li to Mg does improve the elastic properties of the resulting alloys; however it does not necessarily increase the symmetry. Five structures are found which belong to the convex hull, three of which are previously unreported. The second DFT study seeks to understand the electronic environment within lead sulfur (PbS) semiconductor nano-structures and utilizes the open-source Octopus code, designed for electron-ion dynamics in finite systems using time-dependent DFT in real time and real space and which has also been bench-marked extensively [2]. The aim of the second study is to understand at the most fundamental levels the impact reduced symmetry has on the electronic states and transitions at the level of the individual IR-light-absorbing quantum dot. We employ three toy models to isolate the impacts of reduced coordination, Pb-rich structures, and Peierls distortions. An in-depth analysis of the bonding through the charge density and electron localization function shows that the metavalent bonding observed in bulk PbS persists in the nanoscale regime. Changing the stoichiometry too far away from Pb:S = 1:1 results in the loss of semiconducting character and an overall metallic character prevails. When we place particular attention on the effects of atomic coordination, we observe enhanced electron localization clustered around the lowest coordinated atoms. Peierls distortions intensify the clustering behavior which lowers the energy of the occupied electronic states and increases the energy of the unoccupied states as deduced from density of states plots. The change in the electron localization is substantial only for a significant amount of low-coordinated atoms. A conclusion is made with an outlook to future work

Impact of demographic factors on recognition of persons with depression and anxiety in primary care in Slovenia

Background: Research has repeatedly shown that family physicians fail to diagnose up to 70% of patients with common mental disorders. Objective of the study is to investigate associations between persons' gender, age and educational level and detection of depression and anxiety by their family physicians.Methods: We compared the results of two independent observational studies that were performed at the same time on a representative sample of family medicine practice attendees in Slovenia. 10710 patients participated in Slovenian Cross-sectional survey and 1118 patients participated in a first round of a cohort study (PREDICT-D study). Logistic regression was used to examine the effects of age, gender and educational level on detection of depression and anxiety.Results: The prevalence of major depression and Other Anxiety Syndrome (OAS) amongst family practice attendees was low. The prevalence of Panic Syndrome (PS) was comparable to rates reported in the literature. A statistical model with merged data from both studies showed that it was over 15 times more likely for patients with ICD-10 criteria depression to be detected in PREDICT-D study as in SCS survey. In PREDICT-D study it was more likely for people with higher education to be diagnosed with ICD-10 criteria depression than in SCS survey.Conclusion: People with higher levels of education should probably be interviewed in a more standardized way to be recognised as having depression by Slovenian family physicians. This finding requires further validation

Design and Calibration of a Lightweight Physics-Based Model for Fluid-Mediated Self-Assembly of Robotic Modules

In this paper, we consider a system consisting of multiple floating robotic modules performing self-assembly. Faithfully modeling such a system and its inter-module interactions typically involves capturing the hydrodynamic forces acting on the modules using computationally expensive fluid dynamic modeling tools. This poses restrictions on the usability of the resulting models. Here, we present a new approach towards modeling such systems. First, we show how the hardware and firmware of the robotic modules can be faithfully modeled in a high-fidelity robotic simulator. Second, we develop a physics plugin to recreate the hydrodynamic forces acting on the modules and propose a trajectory-based method for calibrating the plugin model parameters. Our calibration method employs a Particle Swarm Optimization (PSO) algorithm, and consists of minimizing the difference between Mean Squared Displacement (MSD) data extracted from real and simulated trajectories of multiple robotic modules

Diversity and distribution of co-infecting Botryosphaeriaceae from Eucalyptus grandis and Syzygium cordatum in South Africa

Species in the fungal family Botryosphaeriaceae are latent pathogens on woody trees. These fungi often have a wide host range, which can include native and introduced hosts in an area. Multi-locus DNA sequence identification on a recent collection of Botryosphaeriaceae from Eucalyptus grandis and Syzygium cordatum trees in South Africa revealed cross-infectivity of several species, novel host associations and new country reports. Neofusicoccum eucalyptorum, Neofusicoccum kwambonambiense, Neofusicoccum parvum, Neofusicoccum australe and Lasiodiplodia pseudotheobromae were identified from both tree species, with L. pseudotheobromae and N. eucalyptorum isolated for the first time from S. cordatum, similar to N. kwambonambiense from Eucalyptus. This also represents the first report of L. pseudotheobromae from South Africa. Botryosphaeriaceae species on Eucalyptus species and S. cordatum are fairly well known from South Africa. However, this study revealed new associations, indicating that conclusions should not be generalized and that more intensive sampling from different areas and over time is likely to reveal distinct species and host association patterns.The National Research Foundation (NRF), members of the Tree Protection Co-operative Programme (TPCP) and the Department of Science and Technology (DST)/NRF Centre of Excellence in Tree Health Biotechnology (CTHB), South Africa. Open Access funded by SAAB.http://www.elsevier.com/locate/sajbhb2016Forestry and Agricultural Biotechnology Institute (FABI)Genetic

Human Computation and Convergence

Humans are the most effective integrators and producers of information, directly and through the use of information-processing inventions. As these inventions become increasingly sophisticated, the substantive role of humans in processing information will tend toward capabilities that derive from our most complex cognitive processes, e.g., abstraction, creativity, and applied world knowledge. Through the advancement of human computation - methods that leverage the respective strengths of humans and machines in distributed information-processing systems - formerly discrete processes will combine synergistically into increasingly integrated and complex information processing systems. These new, collective systems will exhibit an unprecedented degree of predictive accuracy in modeling physical and techno-social processes, and may ultimately coalesce into a single unified predictive organism, with the capacity to address societies most wicked problems and achieve planetary homeostasis.Comment: Pre-publication draft of chapter. 24 pages, 3 figures; added references to page 1 and 3, and corrected typ

Greater impairment of postprandial triacylglycerol than glucose response in metabolic syndrome subjects with fasting hyperglycaemia

Abstract Objective: Studies have started to question whether a specific component or combinations of metabolic syndrome (MetS) components may be more important in relation to cardiovascular disease risk. Our aim was to examine the impact of the presence of raised fasting glucose as a MetS component on postprandial lipaemia. Methods: Men classified with the MetS underwent a sequential test meal investigation, in which blood samples were taken at regular intervals after a test breakfast (t=0 min) and lunch (t=330 min). Lipids, glucose and insulin were measured in the fasting and postprandial samples. Results: MetS subjects with 3 or 4 components were subdivided into those without (n=34) and with (n=23) fasting hyperglycaemia (≥ 5.6 mmol/l), irrespective of the combination of components. Fasting lipids and insulin were similar in the two groups, with glucose significantly higher in the men with glucose as a MetS component (P<0.001). Following the test meals, there was a higher maximum concentration (maxC), area under the curve (AUC) and incremental AUC (P≤0.016) for the postprandial triacylglycerol (TAG) response in men with fasting hyperglycaemia. Greater glucose AUC (P<0.001) and insulin maxC (P=0.010) was also observed in these individuals after the test meals. Multivariate regression analysis revealed fasting glucose to be an important predictor of the postprandial TAG and glucose response. Conclusion: Our data analysis has revealed a greater impairment of postprandial TAG than glucose response in MetS subjects with raised fasting glucose. The worsening of postprandial lipaemic control may contribute to the greater CVD risk reported in individuals with MetS component combinations which include hyperglycaemia

Diversity, phylogeny and pathogenicity of Botryosphaeriaceae on nonnative Eucalyptus grown in an urban environment : a case study

The Botryosphaeriaceae are opportunistic pathogens mostly of woody plants, including Eucalyptus. These fungi can cause cankers and die-back diseases on non-native Eucalyptus trees in South African plantations. Botryosphaeriaceae were isolated from diseased and asymptomatic twigs and leaves from 20 Eucalyptus spp. grown in a Pretoria, South Africa arboretum and its surroundings. The isolates were initially grouped based on conidial morphology and Internal Transcribed Spacer (ITS) rDNA PCR-RFLP profiles. They were further identified using DNA sequence data for the ITS rDNA and translation elongation factor 1-α (TEF-1α) gene regions and tested for pathogenicity. Five species were identified including Botryosphaeria dothidea and four Neofusicoccum species namely Neofusicoccum parvum; N. cryptoaustrale and N. ursorum that were recently described from plant tissues collected as a part of the current study; and Neofusicoccum eucalypti (Winter) Maleme, Pavlic & Slippers comb. nov. The latter species is recorded for the first time on Eucalyptus in South Africa. Most of the identified species were collected from the leaves of 17 different Eucalyptus spp. Neofusicoccum parvum was most commonly isolated (72% of all isolates) followed by B. dothidea species complex (17%). With exception of N. parvum which was isolated from majority of Eucalyptus spp. the other species were isolated from limited number of Eucalyptus species indicating host-preferences. All the isolated Botryosphaeriaceae species produced lesions on inoculated Eucalyptus grandis plants that were significantly larger than those associated with the controls.The National Research Foundation (NRF), members of the Tree Protection Co-operative Programme (TPCP), Department of Science and technology (DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB), South Africa, Department of Water affairs and Forestry, South Africa.http://www.elsevier.com/locate/ufug2018-08-30hj2017Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Monitoring plant functional diversity from space

The world’s ecosystems are losing biodiversity fast. A satellite mission designed to track changes in plant functional diversity around the globe could deepen our understanding of the pace and consequences of this change and how to manage it