Factorizations of and by powers of complete graphs

Let K-k(d) denote the Cartesian product of d copies of the complete graph K-k. We prove necessary and sufficient conditions for the existence of a K-k(r)-factorization of K-pn(s), where p is prime and k > 1, n, r and s are positive integers. (C) 2002 Elsevier Science B.V. All rights reserved.

A conjecture on small embeddings of partial Steiner triple systems

A well-known, and unresolved, conjecture states that every partial Steiner triple system of order u can be embedded in a Steiner triple system of order v for all v equivalent to 1 or 3 (mod 6), v greater than or equal to 2u + 1. However, some partial Steiner triple systems of order u can be embedded in Steiner triple systems of order v < 2u + 1. A more general conjecture that considers these small embeddings is presented and verified for some cases. (C) 2002 Wiley Periodicals, Inc.

Local complexity of Delone sets and crystallinity

This paper characterizes when a Delone set X in R-n is an ideal crystal in terms of restrictions on the number of its local patches of a given size or on the heterogeneity of their distribution. For a Delone set X, let N-X (T) count the number of translation-inequivalent patches of radius T in X and let M-X (T) be the minimum radius such that every closed ball of radius M-X(T) contains the center of a patch of every one of these kinds. We show that for each of these functions there is a gap in the spectrum of possible growth rates between being bounded and having linear growth, and that having sufficiently slow linear growth is equivalent to X being an ideal crystal. Explicitly, for N-X (T), if R is the covering radius of X then either N-X (T) is bounded or N-X (T) greater than or equal to T/2R for all T > 0. The constant 1/2R in this bound is best possible in all dimensions. For M-X(T), either M-X(T) is bounded or M-X(T) greater than or equal to T/3 for all T > 0. Examples show that the constant 1/3 in this bound cannot be replaced by any number exceeding 1/2. We also show that every aperiodic Delone set X has M-X(T) greater than or equal to c(n)T for all T > 0, for a certain constant c(n) which depends on the dimension n of X and is > 1/3 when n > 1.

Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human

By spliced alignment of human DNA and transcript sequence data we constructed a data set of transcript-confirmed exons and introns from 2793 genes, 796 of which (28%) were seen to have multiple isoforms. We find that over one-third of human exons can translate in more than one frame, and that this is highly correlated with G+C content. Introns containing adenosine at donor site position +3 (A3), rather than guanosine (G3), are more common in low G+C regions, while the converse is true in high G+C regions. These two classes of introns are shown to have distinct lengths, consensus sequences and correlations among splice signals, leading to the hypothesis that A3 donor sites are associated with exon definition, and G3 donor sites with intron definition. Minor classes of introns, including GC-AG, U12-type GT-AG, weak, and putative AG-dependant introns are identified and characterized. Cassette exons are more prevalent in low G+C regions, while exon isoforms are more prevalent in high G+C regions. Cassette exon events outnumber other alternative events, while exon isoform events involve truncation twice as often as extension, and occur at acceptor sites twice as often as at donor sites. Alternative splicing is usually associated with weak splice signals, and in a majority of cases, preserves the coding frame. The reported characteristics of constitutive and alternative splice signals, and the hypotheses offered regarding alternative splicing and genome organization, have important implications for experimental research into RNA processing. The 'AltExtron' data sets are available at http://www.bit.uq.edu.au/altExtron/ and http://www.ebi.ac.uk/similar tothanaraj/altExtron/.

Boundary value problems for systems of difference equations associated with systems of second-order ordinary differential equations

We study difference equations which arise as discrete approximations to two-point boundary value problems for systems of second-order ordinary differential equations. We formulate conditions which guarantee a priori bounds on first differences of solutions to the discretized problem. We establish existence results for solutions to the discretized boundary value problems subject to nonlinear boundary conditions. We apply our results to show that solutions to the discrete problem converge to solutions of the continuous problem in an aggregate sense. (C) 2002 Elsevier Science Ltd. All rights reserved.

Existence of multiple solutions for second-order discrete boundary value problems

We give conditions on f involving pairs of discrete lower and discrete upper solutions which lead to the existence of at least three solutions of the discrete two-point boundary value problem yk+1 - 2yk + yk-1 + f (k, yk, vk) = 0, for k = 1,..., n - 1, y0 = 0 = yn,, where f is continuous and vk = yk - yk-1, for k = 1,..., n. In the special case f (k, t, p) = f (t) greater than or equal to 0, we give growth conditions on f and apply our general result to show the existence of three positive solutions. We give an example showing this latter result is sharp. Our results extend those of Avery and Peterson and are in the spirit of our results for the continuous analogue. (C) 2002 Elsevier Science Ltd. All rights reserved.

Fixed point theorems of upper semicontinuous multivalued mappings with applications in hyperconvex metric spaces

In the present paper, we establish two fixed point theorems for upper semicontinuous multivalued mappings in hyperconvex metric spaces and apply these to study coincidence point problems and minimax problems. (C) 2002 Elsevier Science (USA). All rights reserved.

Estimating and evaluating the statistics of gapped local-alignment scores

We present a novel maximum-likelihood-based algorithm for estimating the distribution of alignment scores from the scores of unrelated sequences in a database search. Using a new method for measuring the accuracy of p-values, we show that our maximum-likelihood-based algorithm is more accurate than existing regression-based and lookup table methods. We explore a more sophisticated way of modeling and estimating the score distributions (using a two-component mixture model and expectation maximization), but conclude that this does not improve significantly over simply ignoring scores with small E-values during estimation. Finally, we measure the classification accuracy of p-values estimated in different ways and observe that inaccurate p-values can, somewhat paradoxically, lead to higher classification accuracy. We explain this paradox and argue that statistical accuracy, not classification accuracy, should be the primary criterion in comparisons of similarity search methods that return p-values that adjust for target sequence length.

Control of chaotic instabilities in a spinning spacecraft with dissipation using Lyapunov's method

Control of chaotic instability in a simplified model of a spinning spacecraft with dissipation is achieved using an algorithm derived using Lyapunov's second method. The control method is implemented on a realistic spacecraft parameter configuration which has been found to exhibit chaotic instability for a range of forcing amplitudes and frequencies when a sinusoidally varying torque is applied to the spacecraft. Such a torque, may arise in practice from an unbalanced rotor or from vibrations in appendages. Numerical simulations are performed and the results are studied by means of time history, phase space, Poincare map, Lyapunov characteristic exponents and bifurcation diagrams. (C) 2002 Elsevier Science Ltd. All rights reserved.

A monolithic smoothing-gap algorithm for contact-impact based on the signed distance function

A new algorithm has been developed for smoothing the surfaces in finite element formulations of contact-impact. A key feature of this method is that the smoothing is done implicitly by constructing smooth signed distance functions for the bodies. These functions are then employed for the computation of the gap and other variables needed for implementation of contact-impact. The smoothed signed distance functions are constructed by a moving least-squares approximation with a polynomial basis. Results show that when nodes are placed on a surface, the surface can be reproduced with an error of about one per cent or less with either a quadratic or a linear basis. With a quadratic basis, the method exactly reproduces a circle or a sphere even for coarse meshes. Results are presented for contact problems involving the contact of circular bodies. Copyright (C) 2002 John Wiley Sons, Ltd.

Practical scheme for quantum computation with any two-qubit entangling gate

Which gates are universal for quantum computation? Although it is well known that certain gates on two-level quantum systems (qubits), such as the controlled-NOT, are universal when assisted by arbitrary one-qubit gates, it has only recently become clear precisely what class of two-qubit gates is universal in this sense. We present an elementary proof that any entangling two-qubit gate is universal for quantum computation, when assisted by one-qubit gates. A proof of this result for systems of arbitrary finite dimension has been provided by Brylinski and Brylinski; however, their proof relies on a long argument using advanced mathematics. In contrast, our proof provides a simple constructive procedure which is close to optimal and experimentally practical.

Branching processes and computational collapse of discretized unimodal mappings

In computer simulations of smooth dynamical systems, the original phase space is replaced by machine arithmetic, which is a finite set. The resulting spatially discretized dynamical systems do not inherit all functional properties of the original systems, such as surjectivity and existence of absolutely continuous invariant measures. This can lead to computational collapse to fixed points or short cycles. The paper studies loss of such properties in spatial discretizations of dynamical systems induced by unimodal mappings of the unit interval. The problem reduces to studying set-valued negative semitrajectories of the discretized system. As the grid is refined, the asymptotic behavior of the cardinality structure of the semitrajectories follows probabilistic laws corresponding to a branching process. The transition probabilities of this process are explicitly calculated. These results are illustrated by the example of the discretized logistic mapping.

Further decompositions of complete tripartite graphs into 5-cycles

Let K(r,s,t) denote the complete tripartite graph with partite sets of sizes r, s and t, where r less than or equal to s less than or equal to t. Necessary and sufficient conditions are given for decomposability of K(r, s, t) into 5-cycles whenever r, s and t are all even. This extends work done by Mahmoodian and Mirza-khani (Decomposition of complete tripartite graphs into 5-cycles, in: Combinatorics Advances, Kluwer Academic Publishers, Netherlands, 1995, pp. 235-241) and Cavenagh and Billington. (C) 2002 Elsevier Science B.V. All rights reserved.