A study of the entanglement in systems with periodic boundary conditions

We define the local periodic linking number, LK, between two oriented closed or open chains in a system with three-dimensional periodic boundary conditions. The properties of LK indicate that it is an appropriate measure of entanglement between a collection of chains in a periodic system. Using this measure of linking to assess the extent of entanglement in a polymer melt we study the effect of CReTA algorithm on the entanglement of polyethylene chains. Our numerical results show that the statistics of the local periodic linking number observed for polymer melts before and after the application of CReTA are the same.Comment: 11 pages, 11 figure

On the push&pull protocol for rumour spreading

The asynchronous push&pull protocol, a randomized distributed algorithm for spreading a rumour in a graph $G$, works as follows. Independent Poisson clocks of rate 1 are associated with the vertices of $G$. Initially, one vertex of $G$ knows the rumour. Whenever the clock of a vertex $x$ rings, it calls a random neighbour $y$: if $x$ knows the rumour and $y$ does not, then $x$ tells $y$ the rumour (a push operation), and if $x$ does not know the rumour and $y$ knows it, $y$ tells $x$ the rumour (a pull operation). The average spread time of $G$ is the expected time it takes for all vertices to know the rumour, and the guaranteed spread time of $G$ is the smallest time $t$ such that with probability at least $1-1/n$, after time $t$ all vertices know the rumour. The synchronous variant of this protocol, in which each clock rings precisely at times $1,2,\dots$, has been studied extensively. We prove the following results for any $n$-vertex graph: In either version, the average spread time is at most linear even if only the pull operation is used, and the guaranteed spread time is within a logarithmic factor of the average spread time, so it is $O(n\log n)$. In the asynchronous version, both the average and guaranteed spread times are $\Omega(\log n)$. We give examples of graphs illustrating that these bounds are best possible up to constant factors. We also prove theoretical relationships between the guaranteed spread times in the two versions. Firstly, in all graphs the guaranteed spread time in the asynchronous version is within an $O(\log n)$ factor of that in the synchronous version, and this is tight. Next, we find examples of graphs whose asynchronous spread times are logarithmic, but the synchronous versions are polynomially large. Finally, we show for any graph that the ratio of the synchronous spread time to the asynchronous spread time is $O(n^{2/3})$.Comment: 25 page

The strange-quark chemical potential as an experimentally accessible "order parameter" of the deconfinement phase transition for finite baryon-density

We consider the change of the strange-quark chemical potential in the phase diagram of nuclear matter, employing the Wilson loop and scalar quark condensate order parameters, mass-scaled partition functions and enforcing flavor conservation. Assuming the region beyond the hadronic phase to be described by massive, correlated and interacting quarks, in the spirit of lattice and effective QCD calculations, we find the strange-quark chemical potential to change sign: from positive in the hadronic phase - to zero upon deconfinement - to negative in the partonic domain. We propose this change in the sign of the strange-quark chemical potential to be an experimentally accessible order parameter and a unique, concise and well-defined indication of the quark-deconfinement phase transition in nuclear matter.Comment: 22 pages, 14 figures within text, 2 figures(6,B3) as separate files. To be published in J.Phys.G: Nucl.&Part.Phys. G28 (2002

Integrated Text Mining and Chemoinformatics Analysis Associates Diet to Health Benefit at Molecular Level

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MESSI: metabolic engineering target selection and best strain identification tool

Metabolic engineering and synthetic biology are synergistically related fields for manipulating target pathways and designing microorganisms that can act as chemical factories. Saccharomyces cerevisiae’s ideal bioprocessing traits make yeast a very attractive chemical factory for production of fuels, pharmaceuticals, nutraceuticals as well as a wide range of chemicals. However, future attempts of engineering S. cerevisiae’s metabolism using synthetic biology need to move towards more integrative models that incorporate the high connectivity of metabolic pathways and regulatory processes and the interactions in genetic elements across those pathways and processes. To contribute in this direction, we have developed Metabolic Engineering target Selection and best Strain Identification tool (MESSI), a web server for predicting efficient chassis and regulatory components for yeast bio-based production. The server provides an integrative platform for users to analyse ready-to-use public high-throughput metabolomic data, which are transformed to metabolic pathway activities for identifying the most efficient S. cerevisiae strain for the production of a compound of interest. As input MESSI accepts metabolite KEGG IDs or pathway names. MESSI outputs a ranked list of S. cerevisiae strains based on aggregation algorithms. Furthermore, through a genome-wide association study of the metabolic pathway activities with the strains’ natural variation, MESSI prioritizes genes and small variants as potential regulatory points and promising metabolic engineering targets. Users can choose various parameters in the whole process such as (i) weight and expectation of each metabolic pathway activity in the final ranking of the strains, (ii) Weighted AddScore Fuse or Weighted Borda Fuse aggregation algorithm, (iii) type of variants to be included, (iv) variant sets in different biological levels. Database URL: http://sbb.hku.hk/MESSI

Model of Centauro and strangelet production in heavy ion collisions

We discuss the phenomenological model of Centauro event production in relativistic nucleus-nucleus collisions. This model makes quantitative predictions for kinematic observables, baryon number and mass of the Centauro fireball and its decay products. Centauros decay mainly to nucleons, strange hyperons and possibly strangelets. Simulations of Centauro events for the CASTOR detector in Pb-Pb collisions at LHC energies are performed. The signatures of these events are discussed in detail.Comment: 19 pages, LaTeX+revtex4, 14 eps-figures and 3 table

Ethical and practical challenges in implementing informed consent in HIV/AIDS clinical trials in developing or resource-limited countries

Background/rationale: Ethical issues regarding HIV/AIDS human research in the developing world remain under continuous evaluation; a critical area of concern includes informed consent. This paper reviews several of the most important ethical and practical aspects of informed consent in HIV research in developing countries. Enhancement of overall understanding of such key issues might promote higher ethical standards of future research.Objectives: The major objective was to address informed consent in human research in non-Western societies, and specifically in HIV clinical trials of affected adults. Secondary end-points included the consent complexities in HIV research involving vulnerable patient populations in resource-limited nations, such as children, adolescents and women.Methods: A systematic review of the published literature using MEDLINE and EMBASE from 1998 until December 2008 was performed, using the search terms ‘HIV/AIDS’, ‘informed consent’, ‘clinical trials’, ‘developing world’.Results: Ethical complexities such as participants’ diminished autonomy, coercion or monetary inducement, language difficulties, illiteracy or lack of true understanding of the entire study, cultural barriers mainly due to communitarianism and social diversities were identified in the 44 studies reviewed. Informed consent of vulnerable patient populations must be tailored to their sex and developmental age, while counselling is fundamental. Children and adolescents’ assent must be ensured. Local language is to be used, while trusted community leaders and local cultural representatives may convey information.Discussion: Despite the heterogeneity of studies, similarities were  identified. Providing adequate and comprehensive information and assessing the true understanding of the research represent fundamental prerequisites. Potential solutions to the critical areas of concern include peer counselling and meetings with local community leaders or local cultural representatives. Conclusions: International investigators of HIV human research should bear in mind these ethical issues and their potential solutions, when trying to ensure ethical research conduct, based on a truly informed and culturally relevant consent