Charge-based quantum computing using single donors in semiconductors

Solid-state quantum computer architectures with qubits encoded using single atoms are now feasible given recent advances in the atomic doping of semiconductors. Here we present a charge qubit consisting of two dopant atoms in a semiconductor crystal, one of which is singly ionized. Surface electrodes control the qubit and a radio-frequency single-electron transistor provides fast readout. The calculated single gate times, of order 50 ps or less, are much shorter than the expected decoherence time. We propose universal one- and two-qubit gate operations for this system and discuss prospects for fabrication and scale up.

Segmenting eukaryotic genomes with the generalized Gibbs sampler

Eukaryotic genomes display segmental patterns of variation in various properties, including GC content and degree of evolutionary conservation. DNA segmentation algorithms are aimed at identifying statistically significant boundaries between such segments. Such algorithms may provide a means of discovering new classes of functional elements in eukaryotic genomes. This paper presents a model and an algorithm for Bayesian DNA segmentation and considers the feasibility of using it to segment whole eukaryotic genomes. The algorithm is tested on a range of simulated and real DNA sequences, and the following conclusions are drawn. Firstly, the algorithm correctly identifies non-segmented sequence, and can thus be used to reject the null hypothesis of uniformity in the property of interest. Secondly, estimates of the number and locations of change-points produced by the algorithm are robust to variations in algorithm parameters and initial starting conditions and correspond to real features in the data. Thirdly, the algorithm is successfully used to segment human chromosome 1 according to GC content, thus demonstrating the feasibility of Bayesian segmentation of eukaryotic genomes. The software described in this paper is available from the author's website (www.uq.edu.au/similar to uqjkeith/) or upon request to the author.

Robustness of mathematical models for biological systems

The robustness of mathematical models for biological systems is studied by sensitivity analysis and stochastic simulations. Using a neural network model with three genes as the test problem, we study robustness properties of synthesis and degradation processes. For single parameter robustness, sensitivity analysis techniques are applied for studying parameter variations and stochastic simulations are used for investigating the impact of external noise. Results of sensitivity analysis are consistent with those obtained by stochastic simulations. Stochastic models with external noise can be used for studying the robustness not only to external noise but also to parameter variations. For external noise we also use stochastic models to study the robustness of the function of each gene and that of the system.

More maximal arcs in Desarguesian projective planes and their geometric structure

In a previous paper R. Mathon gave a new construction method for maximal arcs in finite Desarguesian projective planes via closed sets of conics, as well as giving many new examples of maximal arcs. In the current paper, new classes of maximal arcs are constructed, and it is shown that every maximal arc so constructed gives rise to an infinite class of maximal arcs. Apart from when they are of Denniston type or dual hyperovals, closed sets of conics are shown to give maximal arcs that are not isomorphic to the known constructions. An easy characterisation of when a closed set of conics is of Denniston type is given. Results on the geometric structure of the maximal arcs and their duals are proved, as well as on elements of their collineation stabilisers.

Breadth-first search and the Andrews-Curtis conjecture

Andrews and Curtis conjectured in 1965 that every balanced presentation of the trivial group can be transformed into a standard presentation by a finite sequence of elementary transformations. Recent computational work by Miasnikov and Myasnikov on this problem has been based on genetic algorithms. We show that a computational attack based on a breadth-first search of the tree of equivalent presentations is also viable, and seems to outperform that based on genetic algorithms. It allows us to extract shorter proofs (in some cases, provably shortest) and to consider the length thirteen case for two generators. We prove that, up to equivalence, there is a unique minimum potential counterexample.

Irreducible cyclic presentations of the trivial group

We produce families of irreducible cyclic presentations of the trivial group. These families comprehensively answer questions about such presentations asked by Dunwoody and by Edjvet, Hammond, and Thomas. Our theorems are purely theoretical, but their derivation is based on practical computations. We explain how we chose the computations and how we deduced the theorems.

Reliability measures for local nodes assessment in classification trees

Most of the modem developments with classification trees are aimed at improving their predictive capacity. This article considers a curiously neglected aspect of classification trees, namely the reliability of predictions that come from a given classification tree. In the sense that a node of a tree represents a point in the predictor space in the limit, the aim of this article is the development of localized assessment of the reliability of prediction rules. A classification tree may be used either to provide a probability forecast, where for each node the membership probabilities for each class constitutes the prediction, or a true classification where each new observation is predictively assigned to a unique class. Correspondingly, two types of reliability measure will be derived-namely, prediction reliability and classification reliability. We use bootstrapping methods as the main tool to construct these measures. We also provide a suite of graphical displays by which they may be easily appreciated. In addition to providing some estimate of the reliability of specific forecasts of each type, these measures can also be used to guide future data collection to improve the effectiveness of the tree model. The motivating example we give has a binary response, namely the presence or absence of a species of Eucalypt, Eucalyptus cloeziana, at a given sampling location in response to a suite of environmental covariates, (although the methods are not restricted to binary response data).

Decompositions of complete tripartite graphs into triangles with an edge attached

Let K(r, s, t) denote the complete tripartite graph with partite sets of size r, s and t, where r less than or equal to s less than or equal to t. Let D be the graph consisting of a triangle with an edge attached. We show that K(r, s, t) may be decomposed into copies of D if and only if 4 divides rs + st + rt and t less than or equal to 3rs/(r + s).

Balanced critical sets in Latin squares

In this note we first introduce balanced critical sets and near balanced critical sets in Latin squares. Then we prove that there exist balanced critical sets in the back circulant Latin squares of order 3n for n even. Using this result we decompose the back circulant Latin squares of order 3n, n even, into three isotopic and disjoint balanced critical sets each of size 3n. We also find near balanced critical sets in the back circulant Latin squares of order 3n for n odd. Finally, we examine representatives of each main class of Latin squares of order up to six in order to determine which main classes contain balanced or near balanced critical sets.