Numerical Analysis of Boosting Scheme for Scalable NMR Quantum Computation

Among initialization schemes for ensemble quantum computation beginning at thermal equilibrium, the scheme proposed by Schulman and Vazirani [L. J. Schulman and U. V. Vazirani, in Proceedings of the 31st ACM Symposium on Theory of Computing (STOC'99) (ACM Press, New York, 1999), pp. 322-329] is known for the simple quantum circuit to redistribute the biases (polarizations) of qubits and small time complexity. However, our numerical simulation shows that the number of qubits initialized by the scheme is rather smaller than expected from the von Neumann entropy because of an increase in the sum of the binary entropies of individual qubits, which indicates a growth in the total classical correlation. This result--namely, that there is such a significant growth in the total binary entropy--disagrees with that of their analysis.Comment: 14 pages, 18 figures, RevTeX4, v2,v3: typos corrected, v4: minor changes in PROGRAM 1, conforming it to the actual programs used in the simulation, v5: correction of a typographical error in the inequality sign in PROGRAM 1, v6: this version contains a new section on classical correlations, v7: correction of a wrong use of terminology, v8: Appendix A has been added, v9: published in PR

Multi-membership gene regulation in pathway based microarray analysis

This article is available through the Brunel Open Access Publishing Fund. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowledge in a holistic analytical approach. We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways. Our methodology aims towards establishing the state of individual pathways, by identifying those truly affected by the experimental conditions based on the behaviour of such genes. For that purpose it considers all the pathways in which a gene participates and the general census of gene expression per pathway. Results: We utilise hill climbing, simulated annealing and a genetic algorithm to analyse the consistency of the produced results, through the application of fuzzy adjusted rand indexes and hamming distance. All algorithms produce highly consistent genes to pathways allocations, revealing the contribution of genes to pathway functionality, in agreement with current pathway state visualisation techniques, with the simulated annealing search proving slightly superior in terms of efficiency. Conclusions: We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes.The work was sponsored by the studentship scheme of the School of Information Systems, Computing and Mathematics, Brunel Universit

Deterministic secure direct communication using GHZ states and swapping quantum entanglement

We present a deterministic secure direct communication scheme via entanglement swapping, where a set of ordered maximally entangled three-particle states (GHZ states), initially shared by three spatially separated parties, Alice, Bob and Charlie, functions as a quantum information channel. After ensuring the safety of the quantum channel, Alice and Bob apply a series local operations on their respective particles according to the tripartite stipulation and the secret message they both want to send to Charlie. By three Alice, Bob and Charlie's Bell measurement results, Charlie is able to infer the secret messages directly. The secret messages are faithfully transmitted from Alice and Bob to Charlie via initially shared pairs of GHZ states without revealing any information to a potential eavesdropper. Since there is not a transmission of the qubits carrying the secret message between any two of them in the public channel, it is completely secure for direct secret communication if perfect quantum channel is used.Comment: 9 pages, no figur

Amplification by stochastic interference

A new method is introduced to obtain a strong signal by the interference of weak signals in noisy channels. The method is based on the interference of 1/f noise from parallel channels. One realization of stochastic interference is the auditory nervous system. Stochastic interference may have broad potential applications in the information transmission by parallel noisy channels

Black Hole Spectroscopy: Testing General Relativity through Gravitational Wave Observations

Assuming that general relativity is the correct theory of gravity in the strong field limit, can gravitational wave observations distinguish between black hole and other compact object sources? Alternatively, can gravitational wave observations provide a test of one of the fundamental predictions of general relativity? Here we describe a definitive test of the hypothesis that observations of damped, sinusoidal gravitational waves originated from a black hole or, alternatively, that nature respects the general relativistic no-hair theorem. For astrophysical black holes, which have a negligible charge-to-mass ratio, the black hole quasi-normal mode spectrum is characterized entirely by the black hole mass and angular momentum and is unique to black holes. In a different theory of gravity, or if the observed radiation arises from a different source (e.g., a neutron star, strange matter or boson star), the spectrum will be inconsistent with that predicted for general relativistic black holes. We give a statistical characterization of the consistency between the noisy observation and the theoretical predictions of general relativity, together with a numerical example.Comment: 19 pages, 7 figure

Genome Sizes and the Benford Distribution

BACKGROUND: Data on the number of Open Reading Frames (ORFs) coded by genomes from the 3 domains of Life show the presence of some notable general features. These include essential differences between the Prokaryotes and Eukaryotes, with the number of ORFs growing linearly with total genome size for the former, but only logarithmically for the latter. RESULTS: Simply by assuming that the (protein) coding and non-coding fractions of the genome must have different dynamics and that the non-coding fraction must be particularly versatile and therefore be controlled by a variety of (unspecified) probability distribution functions (pdf's), we are able to predict that the number of ORFs for Eukaryotes follows a Benford distribution and must therefore have a specific logarithmic form. Using the data for the 1000+ genomes available to us in early 2010, we find that the Benford distribution provides excellent fits to the data over several orders of magnitude. CONCLUSIONS: In its linear regime the Benford distribution produces excellent fits to the Prokaryote data, while the full non-linear form of the distribution similarly provides an excellent fit to the Eukaryote data. Furthermore, in their region of overlap the salient features are statistically congruent. This allows us to interpret the difference between Prokaryotes and Eukaryotes as the manifestation of the increased demand in the biological functions required for the larger Eukaryotes, to estimate some minimal genome sizes, and to predict a maximal Prokaryote genome size on the order of 8-12 megabasepairs. These results naturally allow a mathematical interpretation in terms of maximal entropy and, therefore, most efficient information transmission

Intracellular interferons in fish : a unique means to combat viral infection

Peer reviewedPublisher PD

Qualitative evaluation of coronary atherosclerosis in a large cohort of young and middle-aged Dutch tissue donors implies that coronary thrombo-embolic manifestations are stochastic

Vascular Surger

Generalized DNA Barcode Design Based on Hamming Codes

The diversity and scope of multiplex parallel sequencing applications is steadily increasing. Critically, multiplex parallel sequencing applications methods rely on the use of barcoded primers for sample identification, and the quality of the barcodes directly impacts the quality of the resulting sequence data. Inspection of the recent publications reveals a surprisingly variable quality of the barcodes employed. Some barcodes are made in a semi empirical fashion, without quantitative consideration of error correction or minimal distance properties. After systematic comparison of published barcode sets, including commercially distributed barcoded primers from Illumina and Epicentre, methods for improved, Hamming code-based sequences are suggested and illustrated. Hamming barcodes can be employed for DNA tag designs in many different ways while preserving minimal distance and error-correcting properties. In addition, Hamming barcodes remain flexible with regard to essential biological parameters such as sequence redundancy and GC content. Wider adoption of improved Hamming barcodes is encouraged in multiplex parallel sequencing applications

Daylight quantum key distribution over 1.6 km

Quantum key distribution (QKD) has been demonstrated over a point-to-point $\sim1.6$-km atmospheric optical path in full daylight. This record transmission distance brings QKD a step closer to surface-to-satellite and other long-distance applications.Comment: 4 pages, 2 figures, 1 table. Submitted to PRL on 14 January 2000 for publication consideratio