The covarion model of molecular evolution : a thesis presented in partial fulfilment of the requirements for the degree of Master of Philosophy in Biology at Massey University

Current methods for constructing evolutionary trees generally do not work well for sequences in which multiple substitutions have occurred. The covarion hypothesis may provide a solution to this problem. This hypothesis states that only a limited number of the codons in a given sequence are free to vary, but that the set of variable codons may change as mutations are fixed in the population. Although this is reasonable from a biological point of view, it is a difficult hypothesis to test scientifically because the apparent large number of parameters involved makes it very hard to analyse statistically. In this study, computer simulations were carried out on up to 51 machines running in parallel, using a simple covarion model based on a hidden Markov model (HMM) approach. This model required two new parameters—the proportion of sites that are variable at any given time, and the rate of exchange between fixed and variable states. These two parameters were both varied in the simulations. Sequence and distance data were simulated on a given tree under this covarion model, and these data were used to test the performance of standard tree-building methods at recovering the original tree The neighbour joining and maximum likelihood methods tested were found to perform better with data generated under the covarion model than with data generated under a simpler model in which all sites vary at the same rate. This suggests that current tree-building methods may perform better with biological data than computer simulation studies suggest

Distributed control of multi-robot systems using bifurcating potential fields

The distributed control of multi-robot systems has been shown to have advantages over conventional single robot systems. These include scalability, flexibility and robustness to failures. This paper considers pattern formation and reconfigurability in a multi-robot system using bifurcating potential fields. It is shown how various patterns can be achieved through a simple free parameter change. In addition the stability of the system of robots is proven to ensure that desired behaviours always occur

Pattern transition in spacecraft formation flying using bifurcating potential field

Many new and exciting space mission concepts have developed around spacecraft formation flying, allowing for autonomous distributed systems that can be robust, scalable and flexible. This paper considers the development of a new methodology for the control of multiple spacecraft. Based on the artificial potential function method, research in this area is extended by considering the new approach of using bifurcation theory as a means of controlling the transition between different formations. For real, safety or mission critical applications it is important to ensure that desired behaviours will occur. Through dynamical systems theory, this paper also aims to provide a step in replacing traditional algorithm validation with mathematical proof, supported through simulation. This is achieved by determining the non-linear stability properties of the system, thus proving the existence or not of desired behaviours. Practical considerations such as the issue of actuator saturation and communication limitations are addressed, with the development of a new bounded control law based on bifurcating potential fields providing the key contribution of this paper. To illustrate spacecraft formation flying using the new methodology formation patterns are considered in low-Earth-orbit utilising the Clohessy-Wiltshire relative linearised equations of motion. It is shown that a formation of spacecraft can be driven safely onto equally spaced projected circular orbits, autonomously reconfiguring between them, whilst satisfying constraints made regarding each spacecraft

Energy efficient mining on a quantum-enabled blockchain using light

We outline a quantum-enabled blockchain architecture based on a consortium of quantum servers. The network is hybridised, utilising digital systems for sharing and processing classical information combined with a fibre--optic infrastructure and quantum devices for transmitting and processing quantum information. We deliver an energy efficient interactive mining protocol enacted between clients and servers which uses quantum information encoded in light and removes the need for trust in network infrastructure. Instead, clients on the network need only trust the transparent network code, and that their devices adhere to the rules of quantum physics. To demonstrate the energy efficiency of the mining protocol, we elaborate upon the results of two previous experiments (one performed over 1km of optical fibre) as applied to this work. Finally, we address some key vulnerabilities, explore open questions, and observe forward--compatibility with the quantum internet and quantum computing technologies.Comment: 25 pages, 5 figure

A fractally fractionated spacecraft

The advantages of decentralised multi-spacecraft architectures for many space applications are well understood. Distributed antennas represent popularly envisaged applications of such an architecture; these are composed of, typically, receiving elements carried on-board multiple spacecraft in precise formation. In this paper decentralised control, based on artificial potential functions, together with a fractal-like connection network, is used to produce autonomous and verifiable deployment and formation control of a swarm of spacecraft into a fractal-like pattern. The effect of using fractal-like routing of control data within the spacecraft generates complex formation shape patterns, while simultaneously reducing the amount of control information required to form such complex formation shapes. Furthermore, the techniques used ensures against swarm fragmentation, which can otherwise be a consequence of the non-uniform connectivity of the communication graph. In particular, the superposition of potential functions operating at multiple levels (single agents, subgroups of agents, groups of agents) according to a self-similar adjacency matrix produces a fractal-like final deployment with the same stability property on each scale. Results from the investigations carried out indicate the approach is feasible, whilst outlining its robustness characteristics, and versatility in formation deployment and control. Considering future high-precision formation flying and control capabilities, this paper considers, for the first time and as an example of a fractally fractionated spacecraft, a decentralised multi-spacecraft fractal shaped antenna. Furthermore, multi-spacecraft architecture exploiting fractal-like formations can be considered to investigate multi-scale phenomena in areas such as cosmic radiation and space plasma physics. Both numerical simulations and analytic treatment are presented, demonstrating the feasibility of deploying and controlling a fractionated fractal antenna in space through autonomous decentralised means. This work frames the problem of architecture and tackles the one of control, whilst not neglecting actuation

Inverse multiobjective optimization: Inferring decision criteria from data

It is a very challenging task to identify the objectives on which a certain decision was based, in particular if several, potentially conflicting criteria are equally important and a continuous set of optimal compromise decisions exists. This task can be understood as the inverse problem of multiobjective optimization, where the goal is to find the objective vector of a given Pareto set. To this end, we present a method to construct the objective vector of a multiobjective optimization problem (MOP) such that the Pareto critical set contains a given set of data points or decision vectors. The key idea is to consider the objective vector in the multiobjective KKT conditions as variable and then search for the objectives that minimize the Euclidean norm of the resulting system of equations. By expressing the objectives in a finite-dimensional basis, we transform this problem into a homogeneous, linear system of equations that can be solved efficiently. There are many important potential applications of this approach. Besides the identification of objectives (both from clean and noisy data), the method can be used for the construction of surrogate models for expensive MOPs, which yields significant speed-ups. Both applications are illustrated using several examples

Verifiable control of a swarm of unmanned aerial vehicles

This article considers the distributed control of a swarm of unmanned aerial vehicles (UAVs) investigating autonomous pattern formation and reconfigurability. A behaviour-based approach to formation control is considered with a velocity field control algorithm developed through bifurcating potential fields. This new approach extends previous research into pattern formation using potential field theory by considering the use of bifurcation theory as a means of reconfiguring a swarm pattern through a free parameter change. The advantage of this kind of system is that it is extremely robust to individual failures, is scalpable, and also flexible. The potential field consists of a steering and repulsive term with the bifurcation of the steering potential resulting in a change of the swarm pattern. The repulsive potential ensures collision avoidance and an equally spaced final formation. The stability of the system is demonstrated to ensure that desired behaviours always occur, assuming that at large separation distances the repulsive potential can be neglected through a scale separation that exists between the steering and repulsive potential. The control laws developed are applied to a formation of ten UAVs using a velocity field tracking approach, where it is shown numerically that desired patterns can be formed safely ensuring collision avoidance

Resistance to multilateral influence on reform : the political backlash against private infrastructure investments

Coercive isomorphism is a prominent source of institutional change. The literature to date has emphasized how actors that are powerful and legitimate (for example, a national government) may coerce the adoption of reforms by dependent actors (for example, state governments and other organizations whose activities are governed by the federal government). The authors observe that an actor's power alone may be sufficient to promote reform, regardless of the actor's legitimacy. But such reforms are more susceptible to subsequent change than those that emerge from processes not subject to the influence of external actors whose sway derives from their power alone. They develop and test their arguments in the context of the worldwide electricity provision industry by analyzing countries'adoption of reforms in response to conditional lending practices by multilateral organizations such as the World Bank and the International Monetary Fund. The authors find that reforms adopted in response to coercive pressures exerted by these organizations encounter much greater resistance, and that the incidence of financial and economic crises, the absence of checks and balances in established political institutions, and the inexperience of investor coalitions dramatically increase the predicted level of resistance.National Governance,Health Monitoring&Evaluation,ICT Policy and Strategies,Politics and Government,Governance Indicators