Asymptotically Optimal Quantum Circuits for d-level Systems

As a qubit is a two-level quantum system whose state space is spanned by |0>, |1>, so a qudit is a d-level quantum system whose state space is spanned by |0>,...,|d-1>. Quantum computation has stimulated much recent interest in algorithms factoring unitary evolutions of an n-qubit state space into component two-particle unitary evolutions. In the absence of symmetry, Shende, Markov and Bullock use Sard's theorem to prove that at least C 4^n two-qubit unitary evolutions are required, while Vartiainen, Moettoenen, and Salomaa (VMS) use the QR matrix factorization and Gray codes in an optimal order construction involving two-particle evolutions. In this work, we note that Sard's theorem demands C d^{2n} two-qudit unitary evolutions to construct a generic (symmetry-less) n-qudit evolution. However, the VMS result applied to virtual-qubits only recovers optimal order in the case that d is a power of two. We further construct a QR decomposition for d-multi-level quantum logics, proving a sharp asymptotic of Theta(d^{2n}) two-qudit gates and thus closing the complexity question for all d-level systems (d finite.) Gray codes are not required, and the optimal Theta(d^{2n}) asymptotic also applies to gate libraries where two-qudit interactions are restricted by a choice of certain architectures.Comment: 18 pages, 5 figures (very detailed.) MatLab files for factoring qudit unitary into gates in MATLAB directory of source arxiv format. v2: minor change

MAVID: Constrained ancestral alignment of multiple sequences

We describe a new global multiple alignment program capable of aligning a large number of genomic regions. Our progressive alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic guide-tree construction, protein based anchoring of ab-initio gene predictions, and constraints derived from a global homology map of the sequences. We have implemented these ideas in the MAVID program, which is able to accurately align multiple genomic regions up to megabases long. MAVID is able to effectively align divergent sequences, as well as incomplete unfinished sequences. We demonstrate the capabilities of the program on the benchmark CFTR region which consists of 1.8Mb of human sequence and 20 orthologous regions in marsupials, birds, fish, and mammals. Finally, we describe two large MAVID alignments: an alignment of all the available HIV genomes and a multiple alignment of the entire human, mouse and rat genomes

Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA)

Based on molecular clock hypothesis, and neutral theory of molecular evolution, molecular phylogenies have been widely used for inferring evolutionary history of organisms and individual genes. Traditionally, alignments and phylogeny trees of proteins and their coding DNA sequences are constructed separately, thus often different conclusions were drawn. Here we present a new strategy for sequence alignment and phylogenetic tree reconstruction, codon and amino acid unified sequence alignment (CAUSA), which aligns DNA and protein sequences and draw phylogenetic trees in a unified manner. We demonstrated that CAUSA improves both the accuracy of multiple sequence alignments and phylogenetic trees by solving a variety of molecular evolutionary problems in virus, bacteria and mammals. Our results support the hypothesis that the molecular clock for proteins has two pointers existing separately in DNA and protein sequences. It is more accurate to read the molecular clock by combination (additive) of these two pointers, since the ticking rates of them are sometimes consistent, sometimes different. CAUSA software were released as Open Source under GNU/GPL license, and are downloadable free of charge from the website www.dnapluspro.com

Fundamental principles in drawing inference from sequence analysis

Individual life courses are dynamic and can be represented as a sequence of states for some portion of their experiences. More generally, study of such sequences has been made in many fields around social science; for example, sociology, linguistics, psychology, and the conceptualisation of subjects progressing through a sequence of states is common. However, many models and sets of data allow only for the treatment of aggregates or transitions, rather than interpreting whole sequences. The temporal aspect of the analysis is fundamental to any inference about the evolution of the subjects but assumptions about time are not normally made explicit. Moreover, without a clear idea of what sequences look like, it is impossible to determine when something is not seen whether it was not actually there. Some principles are proposed which link the ideas of sequences, hypothesis, analytical framework, categorisation and representation; each one being underpinned by the consideration of time. To make inferences about sequences, one needs to: understand what these sequences represent; the hypothesis and assumptions that can be derived about sequences; identify the categories within the sequences; and data representation at each stage. These ideas are obvious in themselves but they are interlinked, imposing restrictions on each other and on the inferences which can be draw