Development of computational methods for electronic structural characterization of strongly correlated materials: from different ab-initio perspectives

The electronic correlations in materials drive a variety of fascinating phenomena from magnetism to metal-to-insulator transitions (MIT), which are due to the coupling between electron spin, charge, ionic displacements, and orbital ordering. Although Density Functional Theory (DFT) successfully describes the electronic structure of weakly interacting material systems, being a static mean-field approach, it fails to predict the properties of Strongly Correlated Materials (SCM) that include transition and rare earth metals where there is a prominent electron localization as in the case of d and f orbitals due to the nature of their spatial confinement. Dynamical Mean Field Theory (DMFT) is a Green’s function based method that has shown success in treating SCM. This dissertation focuses on the development of a user-friendly, open-source Python/Fortran framework, “DMFTwDFT” combining DFT and DMFT to characterize properties of both weakly and strongly correlated materials. The DFT Kohn- Sham orbitals are projected onto Maximally Localized Wannier Functions (MLWF) which essentially maps the Hubbard model to a local impurity model which we solve numerically using quantum Monte Carlo methods to capture both itinerant and localized nature of electrons. Additionally, we provide a library mode for computing the DMFT density matrix which can be linked and internally called from any DFT package allowing developers of other DFT codes to interface with our package and achieve full charge-self-consistency within DFT+DMFT. We then study the stability and diffusion of oxygen vacancies in the correlated material LaNiO3. By treating Ni-d as correlated orbitals along with a Ni-O hybridization manifold, we show that certain configurations undergo a MIT based on the environment of their vacancies. We also compute the transition path energy of a single oxygen vacancy through means of the nudged elastic band (NEB) method. We show that the diffusion energy profile calculated through DFT+U differs from that of DMFT, due to correlation effects that are not quite well captured with static mean-field theories. Additionally, DMFTwDFT was utilized to study strongly correlated alloys and materials useful for neuromorphic computing applications

Cellular and Molecular Pathogenesis of Salmonid Alphavirus 1 in Atlantic Salmon Salmo salar L.

Abstract Salmonid alphaviruses (SAV) are a group of viruses that have recently emerged as a serious threat to the salmonid aquaculture industry in Europe. Over recent years, diseases caused by SAV have severely hampered the Scottish, Irish and Norwegian Atlantic salmon industry, and are considered to be among the major economically important viral diseases affecting the industry at present. Amongst the six subtypes characterised so far, Salmonid alphavirus 1 (SAV1) causes severe pathology in the heart, pancreas and the skeletal muscle of Atlantic salmon leading to death and growth retardation in the affected fish. The biochemical characteristics of the virus and the sequential pathology of the diseases caused by SAV have been described; however the mechanisms responsible for causing the disease and the host defence mechanisms against the virus are poorly defined. This thesis therefore examined the pathogenesis of SAV infection at the cellular and molecular level in vivo in salmon and in vitro in salmonid cells, with a special emphasis on host immune defence mechanisms against the virus. SAV was first isolated from Chinook salmon embryo-214 (CHSE-214) cells in 1995 in Ireland. Several cell lines have since been used to grow the virus. In the present study, three established salmonid cell lines, Chum salmon heart -1 (CHH-1), CHSE-214 and Salmon head kidney -1 (SHK-1) were evaluated for their ability to support the isolation of SAV-1 from infected fish tissue, with CHH-1 cells giving the fastest cytopathic effect (CPE) during primary isolation. The CPE appeared as localised cell-rounding on CHH-1 and CHSE-214 cells, although in SHK-1 cells, the cells were seen to slough off the monolayer relatively later than with the other two cell lines during the infection. The host response to SAV infection was evaluated by experimentally infecting Atlantic salmon parr using a cell culture-adapted virus isolate. A quantitative reverse transcription polymerase chain reaction (qRT-PCR) was developed to examine the virus load in the fish, from which it was found that the highest viral RNA copy number was detected at 5 day post infection (d.p.i), of the 90 day experimental infection period. Characteristic pathological lesions were only seen in the pancreas and the heart but not in the skeletal muscles of the infected fish. A gene expression study using qRT-PCR revealed the rapid induction of interferon (INF) and INF-associated genes in the head kidney of the infected fish compared to the control fish. The Mx protein was found to be highly expressed in the heart and the mucous membranes of infected fish by immunohistochemistry. Interestingly, the pathological changes that were seen occurred some time after the peak expression of genes associated with the INF-1-pathway. When the host-virus interaction of Atlantic salmon infected with SAV was examined using a microarray, a potent first line defence response was observed, together with the signatures of early activation of the adaptive immune response during the initial stages of the infection. Genes associated with transcription, translation and lipid metabolism were significantly differentially expressed in virus infected fish compared to control fish. A large array of antiviral genes was significantly expressed, amongst which were some of the genes also described in mammalian alphavirus infections. Genes associated with apoptosis and anti-apoptosis were also seen to be differentially regulated showing the complexity of the host-virus interaction. Collectively, all of these findings suggest that a non-specific antiviral immune response takes place providing rapid immune protection during the early stages of SAV infection in salmon. In the study on morphogenesis of SAV in salmonid cells using electron microscopy (EM), a rapid internalization of virus into the cells and generation of replication complexes using the secretory pathway of the cell, similar to mammalian alphavirus replication was observed. The mature viruses were released through surface projections, acquiring envelopes from the host cell membrane. From the ultrastructural studies of the salmonid cells infected with SAV, a progressive chromatin marginalisation and condensation could be seen, leading to cellular fragmentation, forming membrane bound apoptotic bodies, characteristic of progressive apoptosis. The activation of caspase-3 in the cytoplasm and genomic DNA damage were also seen in the infected fish cells, indicating that apoptosis is the main cause of cell death during SAV infection. The results of this study have increased our knowledge and understanding of the cellular and molecular mechanisms involved in the pathogenesis of SAV infection, emphasising the importance of the first line defence mechanisms against SAV infection in salmon. This has given an interesting insight into the host mechanisms used to combat the virus during infection, and will undoubtedly be useful for designing new vaccines and management strategies for prevention and control of this important diseas

Trade-offs between retroactivity and noise in connected transcriptional components

At the interconnection of two gene transcriptional components in a biomolecular network, the noise in the downstream component can be reduced by increasing its gene copy number. However, this method of reducing noise increases the load applied to the upstream system, called retroactivity, thereby causing a perturbation in the upstream system. In this work, we quantify the error in the system trajectories caused by perturbations due to retroactivity and noise, and analyze the trade-off between these two perturbations. We model the system as a set of nonlinear chemical Langevin equations and quantify the trade-off by employing contraction theory for stochastic systems.National Science Foundation (U.S.). Division of Computing and Communication Foundations (Award 1058127)United States. Air Force Office of Scientific Research (Award FA9550-12-1-0129

Investigation of the agricultural resources in Sri Lanka

The author has identified the following significant results. Several in-house capabilities were developed. The facilities to prepare color composites of excellent quality were developed, using bulk B/W 70 mm transparencies or 1:1,000,000 positive transparencies. These color composites were studied through optical devices on light tables. A zoom transfer scope was also added, enabling direct transfer of LANDSAT composite data on to base maps

Impact of Organizational Factors on Sales Force Unethical Behavior in the Sri Lankan Life Insurance Industry

As a service providing company the image and the success of the insurance industry vastly depend on the ethical behavior patterns of their salesperson as they are the persons who have direct relationships with customers which in turn build up the customer’s satisfaction and trust towards the organization. Therefore, the managers must have the knowledge of the key determinant of the unethical behavior of their salespersons if they want to ensure the ethical behavior among the salespersons. Different factors contribute to these behavior patterns and organizational factors are more important among them. The main purpose of this research was to identify the organizational factors affecting the unethical behavior patterns of salespersons in the Sri Lankan life insurance industry. An extensive literature review was conducted, and five organizational factors were identified as impacting on unethical behaviour of salespersons in the Sri Lankan life insurance industry. Namely, they were supervisory role, sales targets, organizational culture, code of ethics and a rewarding system. Data were collected from 200 individual salespersons from 10 life insurance companies through structured questionnaires. The stratified random sampling method was used for the selection of the respondents to the sample and data were analyzed using multiple regression. The findings of the research indicated that the supervisory role, sales targets and rewarding system significantly predict the unethical behavior of salespersons. Further, it revealed that sales targets predicted unethical behavior strongly, compared to the rewarding system and the supervisory role. Findings of this research also gave some implications on the code of ethics. It was found that there is no code of ethics in the companies or if exists they are not practiced or enforced. Accordingly, the research provides recommendations that can be used to minimize the unethical behavior patterns of the salespersons. To improve the generalization of the findings, future research should broaden the sample by including general insurance companies and finance companies. Continuing research is needed to analyze the other factors in addition to organizational factors and future research could also look at the customer perspective rather than the salesperson perspective. KeywordsBusiness Ethics; Life Insurance Industry; Organizational Factors; Salesperson; Unethical Behavior Patter

Model reduction for a class of singularly perturbed stochastic differential equations

A class of singularly perturbed stochastic differential equations (SDE) with linear drift and nonlinear diffusion terms is considered. We prove that, on a finite time interval, the trajectories of the slow variables can be well approximated by those of a system with reduced dimension as the singular perturbation parameter becomes small. In particular, we show that when this parameter becomes small the first and second moments of the reduced system's variables closely approximate the first and second moments, respectively, of the slow variables of the singularly perturbed system. Chemical Langevin equations describing the stochastic dynamics of molecular systems with linear propensity functions including both fast and slow reactions fall within the class of SDEs considered here. We therefore illustrate the goodness of our approximation on a simulation example modeling a well known biomolecular system with fast and slow processes.United States. Air Force Office of Scientific Research (Grant FA9550-14-1-0060)National Institute of General Medical Sciences (U.S.) (Grant P50 GMO9879

Demonstration Speech Guidelines

Assignment guidelines for a student assignment on delivering a demonstration speech

Cetacean Presence in the Trincomalee Bay and Adjacent Waters, Sri Lanka

In Sri Lanka thirty species of cetaceans have been recorded to date. The canyon at Trincomalee bay is a multiple submarine canyon complex and anecdotal reports suggest that the Trincomalee bay and its adjacent waters are utilised by a number of cetacean species. Though Cetaceans are known to be abundant in the waters off Trincomalee there is a dearth of research and data pertaining to the abundance and species frequenting the Trincomalee bay and its adjacent waters. As such the current study was initiated, to get a consensus of the abundance and occurrences of species in Trincomalee Bay and its adjacent waters. Field surveys were carried out for 19 months and the research platform was a 35-foot commercial fishing vessel. 177 cetacean encounters were recorded on 67 of the 75 field days. Remarkably a total of 11 species of cetaceans which composed of two species of Baleen Whales and nine species of Toothed Whales were recorded. Delphinidae was the most common family recorded, followed by Balaenopteridae, Ziphiidae, Physeteridae, and Kogiidae. Spinner Dolphins were the most abundant cetacean owing to the large pods observed and the regularity of the sightings. They were the only species seen feeding/traveling with birds and fish (tuna). Sperm Whales, Blue Whales, and Bryde’s Whales were also relatively common. Two records of interspecific association between cetaceans were recorded. The increase in the human population in the study area has resulted in the overexploitation of marine resources which has dire repercussions on the marine mammal communities found in these waters

Localization and tracking of agents for close range applications

This research investigates the state estimation problem in close-range involving multiple targets using Doppler Radar. As the main theme is based on measurements with linear sensor arrays, optimal sensor arrangements are studied for two most popular measurement technologies: Angle-of-Arrival and range based localization systems