A k-means-based formation algorithm for the delay-aware data collection network structure

2014-2015 > Academic research: refereed > Refereed conference paperAccepted ManuscriptPublishe

Stochastic simulations of minimal cells: the Ribocell model

<p>Abstract</p> <p>Background</p> <p>Over the last two decades, lipid compartments (liposomes, lipid-coated droplets) have been extensively used as in vitro "minimal" cell models. In particular, simple and complex biomolecular reactions have been carried out inside these self-assembled micro- and nano-sized compartments, leading to the synthesis of RNA and functional proteins inside liposomes. Despite this experimental progress, a detailed physical understanding of the underlying dynamics is missing. In particular, the combination of solute compartmentalization, reactivity and stochastic effects has not yet been clarified. A combination of experimental and computational approaches can reveal interesting mechanisms governing the behavior of micro compartmentalized systems, in particular by highlighting the intrinsic stochastic diversity within a population of "synthetic cells".</p> <p>Methods</p> <p>In this context, we have developed a computational platform called ENVIRONMENT suitable for studying the stochastic time evolution of reacting lipid compartments. This software - which implements a Gillespie Algorithm - is an improvement over a previous program that simulated the stochastic time evolution of homogeneous, fixed-volume, chemically reacting systems, extending it to more general conditions in which a collection of similar such systems interact and change over the course of time. In particular, our approach is focused on elucidating the role of randomness in the time behavior of chemically reacting lipid compartments, such as micelles, vesicles or micro emulsions, in regimes where random fluctuations due to the stochastic nature of reacting events can lead an open system towards unexpected time evolutions.</p> <p>Results</p> <p>This paper analyses the so-called Ribocell (RNA-based cell) model. It consists in a hypothetical minimal cell based on a self-replicating minimum RNA genome coupled with a self-reproducing lipid vesicle compartment. This model assumes the existence of two ribozymes, one able to catalyze the conversion of molecular precursors into lipids and the second able to replicate RNA strands. The aim of this contribution is to explore the feasibility of this hypothetical minimal cell. By deterministic kinetic analysis, the best external conditions to observe synchronization between genome self-replication and vesicle membrane reproduction are determined, while its robustness to random fluctuations is investigated using stochastic simulations, and then discussed.</p

A k-Means-Based Formation Algorithm for the Delay-Aware Data Collection Network Structure

A wireless sensor network (WSN) consists of a large number of wireless sensor nodes that collect information from their sensing terrain. Wireless sensor nodes are, in general, battery-powered devices with limited processing and transmission power. Therefore, the lifetime of WSNs heavily depends on their energy efficiency. Multiple-cluster 2-hop (MC2H) network structure is commonly used in WSNs to reduce energy consumption due to long-range communications. However, networks with the MC2H network structure are commonly associated with long data collection processes. The delay-aware data collection network structure (DADCNS) is proposed to shorten the duration of data collection processes without sacrificing network lifetime. In this paper, a k-means-based formation algorithm for the DADCNS, namely DADCNS-RK, is proposed. The proposed algorithm can organize a network into the DADCNS, while minimizing the total communication distance among connected sensor nodes by performing k-means clustering recursively. Simulation results show that, when comparing with other DADCNSs formed by different algorithms, the proposed algorithm can reduce the total communication distances of networks significantly.Department of Electronic and Information EngineeringRefereed conference pape

Temporal variation of coastal surface sediment bacterial communities along an environmental pollution gradient

Terminal restriction fragment length polymorphism analysis (T-RFLP) was used to track the changes of bacterial community compositions (BCC) in coastal surface sediments along an environmental pollution gradient between 2004 and 2006. BCC in the chronically contaminated sites showed the largest deviation from those in the adjacent sites. Surprisingly, BCC at two contrasting environments (oceanic vs. river-influenced) were more similar. Unexpectedly, the BCC did not recover (when compared to oceanic control site) even after 5 years of pollution abatement initiatives in Victoria Harbour, Hong Kong. On the other hand, disposal of treated sewage for 5 years in one of the sites did not significantly affect the BCC. A striking seasonal variation in the BCC was observed at only the polluted sites. Although factors other than pollution gradients may explain the observed BCC patterns, the information presented here can be useful in predicting long-term effects of pollution on BCC. Furthermore, this study suggests that BCC analysis using T-RFLP is a faster, reliable and easier approach to monitor microbenthic community response to environmental pollution gradient in coastal sediments. © 2010 Elsevier Ltd.link_to_subscribed_fulltex

Qualitative and quantitative changes in marine biofilms as a function of temperature and salinity in summer and winter

This study examined quantitative (dry weight, chlorophyll a content and C:N ratio) and qualitative (community compositions of bacteria and diatoms) changes in marine biofilms as a function of season (summer 2003 and winter 2004), temperature (16, 23 and 30°C) and salinity (20‰, 27‰ and 34‰) under laboratory conditions. Biofilms were allowed to develop for 20 days in the laboratory, using natural sea water collected from Port Shelter, Hong Kong. The following results were obtained: (1) biofilm dry weight was greater in summer than in winter, and greater at 34‰ than at 20‰; (2) biofilm chlorophyll a content was affected by all three factors (season, temperature and salinity), with significant interactive effects among the three factors; and (3) C:N ratio was affected by season (winter > summer) and temperature (30°C > 16°C in summer), but not by salinity. Bacterial community composition was analyzed by terminal restriction-fragment length polymorphism of polymerase chain reaction-amplified 16S rRNA genes. In summer, community compositions of both bacteria and diatoms were strongly affected by salinity. In addition, natural summer biofilms that developed at three field sites, where different salinities were found, harbored appreciably different bacterial and diatom community compositions. In contrast, in winter, temperature exerted a major influence on community compositions. The present study adds to the growing evidence that environmental factors are important determinants of both the quality and quantity of marine biofilms. © 2006 Cambridge University Press.link_to_subscribed_fulltex

Genotyping and species identification of Fritillaria by DNA chips

2002-2003 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe