Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

Stability analysis and control of multiple converter based autonomous microgrid

In this paper, the stability of an autonomous microgrid with multiple distributed generators (DG) is studied through eigenvalue analysis. It is assumed that all the DGs are connected through Voltage Source Converter (VSC) and all connected loads are passive. The VSCs are controlled by state feedback controller to achieve desired voltage and current outputs that are decided by a droop controller. The state space models of each of the converters with its associated feedback are derived. These are then connected with the state space models of the droop, network and loads to form a homogeneous model, through which the eigenvalues are evaluated. The system stability is then investigated as a function of the droop controller real and reac-tive power coefficients. These observations are then verified through simulation studies using PSCAD/EMTDC. It will be shown that the simulation results closely agree with stability be-havior predicted by the eigenvalue analysis.

Power quality enhanced operation and control of a microgrid based custom power park

This paper describes the operation of a microgrid that contains a custom power park (CPP). The park may contain an unbalanced and/or nonlinear load and the microgrid may contain many dis-tributed generators (DGs). One of the DGs in the microgrid is used as a compensator to achieve load compensation. A new method is proposed for current reference generation for load compensation, which takes into account the real and reactive power to be supplied by the DG connected to the compensator. The real and reactive power from the DGs and the utility source is tightly regulated assuming that dedicated communication channels are available. Therefore this scheme is most suitable in cases where the loads in CPP and DGs are physically located close to each other. The proposal is validated through extensive simulation studies using EMTDC/PSCAD software package (version 4.2).

Power sharing and stability enhancement of an autonomous microgrid with inertial and non-inertial DGs with DSTATCOM

This paper proposes a method of enhancing system stability with a distribution static compensator (DSTATCOM) in an autonomous microgrid with multiple distributed generators (DG). It is assumed that there are both inertial and non-inertial DGs connected to the microgrid. The inertial DG can be a synchronous machine of smaller rating while inertia less DGs (solar) are assumed as DC sources. The inertia less DGs are connected through Voltage Source Converter (VSC) to the microgrid. The VSCs are controlled by either state feedback or current feedback mode to achieve desired voltage-current or power outputs respectively. The power sharing among the DGs is achieved by drooping voltage angle. Once the reference for the output voltage magnitude and angle is calculated from the droop, state feedback controllers are used to track the reference. The angle reference for the synchronous machine is compared with the output voltage angle of the machine and the error is fed to a PI controller. The controller output is used to set the power reference of the synchronous machine. The rate of change in the angle in a synchronous machine is restricted by the machine inertia and to mimic this nature, the rate of change in the VSCs angles are restricted by a derivative feedback in the droop control. The connected distribution static compensator (DSTATCOM) provides ride through capability during power imbalance in the microgrid, especially when the stored energy of the inertial DG is not sufficient to maintain stability. The inclusion of the DSATCOM in such cases ensures the system stability. The efficacies of the controllers are established through extensive simulation studies using PSCAD.

Operation and control of a hybrid microgrid containing unbalanced and nonlinear loads

This paper shows how the power quality can be improved in a microgrid that is supplying a nonlinear and unbalanced load. The microgrid contains a hybrid combination of inertial and converter interfaced distributed generation units where a decentralized power sharing algorithm is used to control its power management. One of the distributed generators in the microgrid is used as a power quality compensator for the unbalanced and harmonic load. The current reference generation for power quality improvement takes into account the active and reactive power to be supplied by the micro source which is connected to the compensator. Depending on the power requirement of the nonlinear load, the proposed control scheme can change modes of operation without any external communication interfaces. The compensator can operate in two modes depending on the entire power demand of the unbalanced nonlinear load. The proposed control scheme can even compensate system unbalance caused by the single-phase micro sources and load changes. The efficacy of the proposed power quality improvement control and method in such a microgrid is validated through extensive simulation studies using PSCAD/EMTDC software with detailed dynamic models of the micro sources and power electronic converters

Enhancing the Stability of an Autonomous Microgrid using DSTATCOM

This paper proposes a method enhancing stability of an autonomous microgrid with distribution static compensator (DSTATCOM) and power sharing with multiple distributed generators (DG). It is assumed that all the DGs are connected through voltage source converter (VSC) and all connected loads are passive, making the microgrid totally inertia less. The VSCs are controlled by either state feedback or current feedback mode to achieve desired voltage-current or power outputs respectively. A modified angle droop is used for DG voltage reference generation. Power sharing ratio of the proposed droop control is established through derivation and verified by simulation results. A DSTATCOM is connected in the microgrid to provide ride through capability during power imbalance in the microgrid, thereby enhancing the system stability. This is established through extensive simulation studies using PSCAD.

Addressing issues in sparseness, ecological bias and formulation of the adjacency matrix in Bayesian spatio-temporal analysis of disease counts

The main objective of this PhD was to further develop Bayesian spatio-temporal models (specifically the Conditional Autoregressive (CAR) class of models), for the analysis of sparse disease outcomes such as birth defects. The motivation for the thesis arose from problems encountered when analyzing a large birth defect registry in New South Wales. The specific components and related research objectives of the thesis were developed from gaps in the literature on current formulations of the CAR model, and health service planning requirements. Data from a large probabilistically-linked database from 1990 to 2004, consisting of fields from two separate registries: the Birth Defect Registry (BDR) and Midwives Data Collection (MDC) were used in the analyses in this thesis. The main objective was split into smaller goals. The first goal was to determine how the specification of the neighbourhood weight matrix will affect the smoothing properties of the CAR model, and this is the focus of chapter 6. Secondly, I hoped to evaluate the usefulness of incorporating a zero-inflated Poisson (ZIP) component as well as a shared-component model in terms of modeling a sparse outcome, and this is carried out in chapter 7. The third goal was to identify optimal sampling and sample size schemes designed to select individual level data for a hybrid ecological spatial model, and this is done in chapter 8. Finally, I wanted to put together the earlier improvements to the CAR model, and along with demographic projections, provide forecasts for birth defects at the SLA level. Chapter 9 describes how this is done. For the first objective, I examined a series of neighbourhood weight matrices, and showed how smoothing the relative risk estimates according to similarity by an important covariate (i.e. maternal age) helped improve the model’s ability to recover the underlying risk, as compared to the traditional adjacency (specifically the Queen) method of applying weights. Next, to address the sparseness and excess zeros commonly encountered in the analysis of rare outcomes such as birth defects, I compared a few models, including an extension of the usual Poisson model to encompass excess zeros in the data. This was achieved via a mixture model, which also encompassed the shared component model to improve on the estimation of sparse counts through borrowing strength across a shared component (e.g. latent risk factor/s) with the referent outcome (caesarean section was used in this example). Using the Deviance Information Criteria (DIC), I showed how the proposed model performed better than the usual models, but only when both outcomes shared a strong spatial correlation. The next objective involved identifying the optimal sampling and sample size strategy for incorporating individual-level data with areal covariates in a hybrid study design. I performed extensive simulation studies, evaluating thirteen different sampling schemes along with variations in sample size. This was done in the context of an ecological regression model that incorporated spatial correlation in the outcomes, as well as accommodating both individual and areal measures of covariates. Using the Average Mean Squared Error (AMSE), I showed how a simple random sample of 20% of the SLAs, followed by selecting all cases in the SLAs chosen, along with an equal number of controls, provided the lowest AMSE. The final objective involved combining the improved spatio-temporal CAR model with population (i.e. women) forecasts, to provide 30-year annual estimates of birth defects at the Statistical Local Area (SLA) level in New South Wales, Australia. The projections were illustrated using sixteen different SLAs, representing the various areal measures of socio-economic status and remoteness. A sensitivity analysis of the assumptions used in the projection was also undertaken. By the end of the thesis, I will show how challenges in the spatial analysis of rare diseases such as birth defects can be addressed, by specifically formulating the neighbourhood weight matrix to smooth according to a key covariate (i.e. maternal age), incorporating a ZIP component to model excess zeros in outcomes and borrowing strength from a referent outcome (i.e. caesarean counts). An efficient strategy to sample individual-level data and sample size considerations for rare disease will also be presented. Finally, projections in birth defect categories at the SLA level will be made.

Benefit analysis of airborne GPS occultation approach : a case study for the Australian region

This paper aims to present a preliminary benefit analysis for airborne GPS occultation technique for the Australian region. The simulation studies are based on current domestic commercial flights between major Australian airports. With the knowledge of GPS satellite ephemeris data, occultation events for for any particular flight can be determined. Preliminary analysis shows a high resolution occultation observations can be achieved with this approach, for instance, about 15 occultation events for a Perth-to-Sydney flight. The simulation result agrees to the results published by other researchers for a different region. Of course, occultation observation during off-peak hours might be affected due to the limited flight activities. --------- High resolution occultation observations obtainable from airborne GPS occultation system provides an opportunity to improve the current global numerical weather prediction (NWP) models and ultimately improves the accuracy in weather forecasting. More intensive research efforts and experimental demonstrations are required in order to demonstrate the technical feasibility of the airborne GPS technology.

Separation management approaches during periods of communication failure

New air traffic automated separation management concepts are constantly under investigation. Yet most of the automated separation management algorithms proposed over the last few decades have assumed either perfect communication or exact knowledge of all aircraft locations. In realistic environments, these idealized assumptions are not valid and any communication failure can potentially lead to disastrous outcomes. This paper examines the separation performance behavior of several popular algorithms during periods of information loss. This comparison is done through simulation studies. These simulation studies suggest that communication failure can cause the performance of these separation management algorithms to degrade significantly. This paper also describes some preliminary flight tests.

Automated centralised separation management with onboard decision support

This paper proposes a novel automated separation management concept in which onboard decision support is integrated within a centralised air traffic separation management system. The onboard decision support system involves a decentralised separation manager that can overrule air traffic management instructions under certain circumstances. This approach allows the advantages of both centralised and decentralised concepts to be combined (and disadvantages of each separation management approach to be mitigated). Simulation studies are used to illustrate the potential benefits of the combined separation management concept.

Bayesian hybrid algorithms and models : implementation and associated issues

This thesis addresses computational challenges arising from Bayesian analysis of complex real-world problems. Many of the models and algorithms designed for such analysis are ‘hybrid’ in nature, in that they are a composition of components for which their individual properties may be easily described but the performance of the model or algorithm as a whole is less well understood. The aim of this research project is to after a better understanding of the performance of hybrid models and algorithms. The goal of this thesis is to analyse the computational aspects of hybrid models and hybrid algorithms in the Bayesian context. The first objective of the research focuses on computational aspects of hybrid models, notably a continuous finite mixture of t-distributions. In the mixture model, an inference of interest is the number of components, as this may relate to both the quality of model fit to data and the computational workload. The analysis of t-mixtures using Markov chain Monte Carlo (MCMC) is described and the model is compared to the Normal case based on the goodness of fit. Through simulation studies, it is demonstrated that the t-mixture model can be more flexible and more parsimonious in terms of number of components, particularly for skewed and heavytailed data. The study also reveals important computational issues associated with the use of t-mixtures, which have not been adequately considered in the literature. The second objective of the research focuses on computational aspects of hybrid algorithms for Bayesian analysis. Two approaches will be considered: a formal comparison of the performance of a range of hybrid algorithms and a theoretical investigation of the performance of one of these algorithms in high dimensions. For the first approach, the delayed rejection algorithm, the pinball sampler, the Metropolis adjusted Langevin algorithm, and the hybrid version of the population Monte Carlo (PMC) algorithm are selected as a set of examples of hybrid algorithms. Statistical literature shows how statistical efficiency is often the only criteria for an efficient algorithm. In this thesis the algorithms are also considered and compared from a more practical perspective. This extends to the study of how individual algorithms contribute to the overall efficiency of hybrid algorithms, and highlights weaknesses that may be introduced by the combination process of these components in a single algorithm. The second approach to considering computational aspects of hybrid algorithms involves an investigation of the performance of the PMC in high dimensions. It is well known that as a model becomes more complex, computation may become increasingly difficult in real time. In particular the importance sampling based algorithms, including the PMC, are known to be unstable in high dimensions. This thesis examines the PMC algorithm in a simplified setting, a single step of the general sampling, and explores a fundamental problem that occurs in applying importance sampling to a high-dimensional problem. The precision of the computed estimate from the simplified setting is measured by the asymptotic variance of the estimate under conditions on the importance function. Additionally, the exponential growth of the asymptotic variance with the dimension is demonstrated and we illustrates that the optimal covariance matrix for the importance function can be estimated in a special case.

Testing of a distributed generation system with a virtual grid

The paper proposes a solution for testing of a physical distributed generation system (DGs) along with a computer simulated network. The computer simulated network is referred as the virtual grid in this paper. Integration of DG with the virtual grid provides broad area of testing of power supplying capability and dynamic performance of a DG. It is shown that a DG can supply a part of load power while keeping Point of Common Coupling (PCC) voltage magnitude constant. To represent the actual load, a universal load along with power regenerative capability is designed with the help of voltage source converter (VSC) that mimics the load characteristic. The overall performance of the proposed scheme is verified using computer simulation studies.

Operation and control of a DVR in the presence of interharmonics

The paper discusses the operating principles and control characteristics of a dynamic voltage restorer (DVR). It is assumed that the source voltages contain interharmonic components in addition to fundamental components. The main aim of the DVR is to produce a set of clean balanced sinusoidal voltages across the load terminals irrespective of unbalance, distortion and voltage sag/swell in the supply voltage. An algorithm has been discussed for extracting fundamental phasor sequence components from the samples of three-phase voltages or current waveforms having integer harmonics and interharmonics. The DVR operation based on extracted components is demonstrated. The switching signal is generated using a deadbeat controller. It has been shown that the DVR is able to compensate these interharmonic components such that the load voltages are perfectly regulated. The DVR operation under deep voltage sag is also discussed. The proposed DVR operation is verified through the computer simulation studies using the MATLAB software package.

Performance study of two different compensating devices in a custom power park

Simulation study of a custom power park (CPP) is presented. It is assumed that the park contains unbalanced and nonlinear loads in addition to a sensitive load. Two different types of compensators are used separately to protect the sensitive load against unbalance and distortion caused by the other loads. It has been shown that a shunt compensator can regulate the voltage of the CPP bus, whereas the series compensator can only regulate the sensitive load terminal voltage. Additional issues such as the load transfer through a static transfer switch, detection of sag/fault etc. are also discussed. The concepts are validated through PSCAD/EMTDC simulation studies on a sample distribution system.

Control schemes for equalization of capacitor voltages in neutral clamped shunt compensator

Voltage imbalance in capacitors is a well-known problem in compensator topologies which use two or more capacitors. This imbalance may exist even if the load does not contain any DC component, due to practical factors. However, when the load contains a DC part, the voltage imbalance problem becomes critical. In this paper, a two-quadrant chopper has been used to regulate the capacitor voltages in a two-capacitor compensator structure. Two different control strategies for the two-quadrant chopper to equalize the voltage of the capacitors have been proposed. The strategies are validated through detailed simulation studies. Experiments have also been carried out to validate the hysteresis control of chopper.