Imp d&e feasibility study

Launching of Interplanetary Monitoring Platform spacecraft into lunar orbi

Nonequilibrium static growing length scales in supercooled liquids on approaching the glass transition

The small wavenumber $k$ behavior of the structure factor $S(k)$ of overcompressed amorphous hard-sphere configurations was previously studied for a wide range of densities up to the maximally random jammed state, which can be viewed as a prototypical glassy state [A. Hopkins, F. H. Stillinger and S. Torquato, Phys. Rev. E, 86, 021505 (2012)]. It was found that a precursor to the glassy jammed state was evident long before the jamming density was reached as measured by a growing nonequilibrium length scale extracted from the volume integral of the direct correlation function $c(r)$, which becomes long-ranged as the critical jammed state is reached. The present study extends that work by investigating via computer simulations two different atomic models: the single-component Z2 Dzugutov potential in three dimensions and the binary-mixture Kob-Andersen potential in two dimensions. Consistent with the aforementioned hard-sphere study, we demonstrate that for both models a signature of the glass transition is apparent well before the transition temperature is reached as measured by the length scale determined from from the volume integral of the direct correlation function in the single-component case and a generalized direct correlation function in the binary-mixture case. The latter quantity is obtained from a generalized Orstein-Zernike integral equation for a certain decoration of the atomic point configuration. We also show that these growing length scales, which are a consequence of the long-range nature of the direct correlation functions, are intrinsically nonequilibrium in nature as determined by an index $X$ that is a measure of deviation from thermal equilibrium. It is also demonstrated that this nonequilibrium index, which increases upon supercooling, is correlated with a characteristic relaxation time scale.Comment: 26 pages, 14 figure

Dynamical mechanism of atrial fibrillation: a topological approach

While spiral wave breakup has been implicated in the emergence of atrial fibrillation, its role in maintaining this complex type of cardiac arrhythmia is less clear. We used the Karma model of cardiac excitation to investigate the dynamical mechanisms that sustain atrial fibrillation once it has been established. The results of our numerical study show that spatiotemporally chaotic dynamics in this regime can be described as a dynamical equilibrium between topologically distinct types of transitions that increase or decrease the number of wavelets, in general agreement with the multiple wavelets hypothesis. Surprisingly, we found that the process of continuous excitation waves breaking up into discontinuous pieces plays no role whatsoever in maintaining spatiotemporal complexity. Instead this complexity is maintained as a dynamical balance between wave coalescence -- a unique, previously unidentified, topological process that increases the number of wavelets -- and wave collapse -- a different topological process that decreases their number.Comment: 15 pages, 14 figure

Application of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data

We present two complementary approaches for the interpretation of clusters of co-regulated genes, such as those obtained from DNA chips and related methods. Starting from a cluster of genes with similar expression profiles, two basic questions can be asked: 1. Which mechanism is responsible for the coordinated transcriptional response of the genes? This question is approached by extracting motifs that are shared between the upstream sequences of these genes. The motifs extracted are putative cis-acting regulatory elements. 2. What is the physiological meaning for the cell to express together these genes? One way to answer the question is to search for potential metabolic pathways that could be catalyzed by the products of the genes. This can be done by selecting the genes from the cluster that code for enzymes, and trying to assemble the catalyzed reactions to form metabolic pathways. We present tools to answer these two questions, and we illustrate their use with selected examples in the yeast Saccharomyces cerevisiae. The tools are available on the web (http://ucmb.ulb.ac.be/bioinformatics/rsa-tools/; http://www.ebi.ac.uk/research/pfbp/; http://www.soi.city.ac.uk/~msch/)

Improving the Price of Anarchy for Selfish Routing via Coordination Mechanisms

We reconsider the well-studied Selfish Routing game with affine latency functions. The Price of Anarchy for this class of games takes maximum value 4/3; this maximum is attained already for a simple network of two parallel links, known as Pigou's network. We improve upon the value 4/3 by means of Coordination Mechanisms. We increase the latency functions of the edges in the network, i.e., if $\ell_e(x)$ is the latency function of an edge $e$, we replace it by $\hat{\ell}_e(x)$ with $\ell_e(x) \le \hat{\ell}_e(x)$ for all $x$. Then an adversary fixes a demand rate as input. The engineered Price of Anarchy of the mechanism is defined as the worst-case ratio of the Nash social cost in the modified network over the optimal social cost in the original network. Formally, if \CM(r) denotes the cost of the worst Nash flow in the modified network for rate $r$ and \Copt(r) denotes the cost of the optimal flow in the original network for the same rate then [\ePoA = \max_{r \ge 0} \frac{\CM(r)}{\Copt(r)}.] We first exhibit a simple coordination mechanism that achieves for any network of parallel links an engineered Price of Anarchy strictly less than 4/3. For the case of two parallel links our basic mechanism gives 5/4 = 1.25. Then, for the case of two parallel links, we describe an optimal mechanism; its engineered Price of Anarchy lies between 1.191 and 1.192.Comment: 17 pages, 2 figures, preliminary version appeared at ESA 201

RepSeq-A database of amino acid repeats present in lower eukaryotic pathogens

BACKGROUND Amino acid repeat-containing proteins have a broad range of functions and their identification is of relevance to many experimental biologists. In human-infective protozoan parasites (such as the Kinetoplastid and Plasmodium species), they are implicated in immune evasion and have been shown to influence virulence and pathogenicity. RepSeq http://repseq.gugbe.com is a new database of amino acid repeat-containing proteins found in lower eukaryotic pathogens. The RepSeq database is accessed via a web-based application which also provides links to related online tools and databases for further analyses. RESULTS The RepSeq algorithm typically identifies more than 98% of repeat-containing proteins and is capable of identifying both perfect and mismatch repeats. The proportion of proteins that contain repeat elements varies greatly between different families and even species (3 - 35% of the total protein content). The most common motif type is the Sequence Repeat Region (SRR) - a repeated motif containing multiple different amino acid types. Proteins containing Single Amino Acid Repeats (SAARs) and Di-Peptide Repeats (DPRs) typically account for 0.5 - 1.0% of the total protein number. Notable exceptions are P. falciparum and D. discoideum, in which 33.67% and 34.28% respectively of the predicted proteomes consist of repeat-containing proteins. These numbers are due to large insertions of low complexity single and multi-codon repeat regions. CONCLUSION The RepSeq database provides a repository for repeat-containing proteins found in parasitic protozoa. The database allows for both individual and cross-species proteome analyses and also allows users to upload sequences of interest for analysis by the RepSeq algorithm. Identification of repeat-containing proteins provides researchers with a defined subset of proteins which can be analysed by expression profiling and functional characterisation, thereby facilitating study of pathogenicity and virulence factors in the parasitic protozoa. While primarily designed for kinetoplastid work, the RepSeq algorithm and database retain full functionality when used to analyse other species

CODA: Accurate Detection of Functional Associations between Proteins in Eukaryotic Genomes Using Domain Fusion

Background: In order to understand how biological systems function it is necessary to determine the interactions and associations between proteins. Gene fusion prediction is one approach to detection of such functional relationships. Its use is however known to be problematic in higher eukaryotic genomes due to the presence of large homologous domain families. Here we introduce CODA (Co-Occurrence of Domains Analysis), a method to predict functional associations based on the gene fusion idiom.Methodology/Principal Findings: We apply a novel scoring scheme which takes account of the genome-specific size of homologous domain families involved in fusion to improve accuracy in predicting functional associations. We show that CODA is able to accurately predict functional similarities in human with comparison to state-of-the-art methods and show that different methods can be complementary. CODA is used to produce evidence that a currently uncharacterised human protein may be involved in pathways related to depression and that another is involved in DNA replication.Conclusions/Significance: The relative performance of different gene fusion methodologies has not previously been explored. We find that they are largely complementary, with different methods being more or less appropriate in different genomes. Our method is the only one currently available for download and can be run on an arbitrary dataset by the user. The CODA software and datasets are freely available from ftp://ftp.biochem.ucl.ac.uk/pub/gene3d_data/v6.1.0/CODA/. Predictions are also available via web services from http://funcnet.eu/

FIRE Arctic Clouds Experiment

An overview is given of the First ISCCP Regional Experiment (FIRE) Arctic Clouds Experiment that was conducted in the Arctic during April through July, 1998. The principal goal of the field experiment was to gather the data needed to examine the impact of arctic clouds on the radiation exchange between the surface, atmosphere, and space, and to study how the surface influences the evolution of boundary layer clouds. The observations will be used to evaluate and improve climate model parameterizations of cloud and radiation processes, satellite remote sensing of cloud and surface characteristics, and understanding of cloud-radiation feedbacks in the Arctic. The experiment utilized four research aircraft that flew over surface-based observational sites in the Arctic Ocean and Barrow, Alaska. In this paper we describe the programmatic and science objectives of the project, the experimental design (including research platforms and instrumentation), conditions that were encountered during the field experiment, and some highlights of preliminary observations, modelling, and satellite remote sensing studies

Hyperpaths in network based on transit schedules

The concept of a hyperpath was introduced for handling passenger strategies in route choice behavior for public transit, especially in a frequency-based transit service environment. This model for handling route choice behavior has been widely used for planning transit services, and hyperpaths are now applied in areas beyond public transit. A hyperpath representing more specific passenger behaviors on a network based on transit schedules is proposed. A link-based time-expanded (LBTE) network for transit schedules is introduced; in the network each link represents a scheduled vehicle trip (or trip segment) with departure time and travel time (or arrival time) between two consecutive stops. The proposed LBTE network reduces the effort to build a network based on transit schedules because the network is expanded with scheduled links. A link-based representation of a hypergraph with existing hyperpath model properties that is directly integrated with the LBTE network is also proposed. Transit passenger behavior was incorporated for transfers in the link-based hyperpath. The efficiency of the proposed hyperpath model was demonstrated. The proposed models were applied on a test network and a real transit network represented by the general specification of Google's transit feed

Hydrogen minority ion cyclotron resonance heating in presence of the iter-like wall in jet

The most recent JET campaign has focused on characterizing operation with the "ITER-like" wall. One of the questions that needed to be answered is whether the auxiliary heating methods do not lead to unacceptably high levels of impurity influx, preventing fusion-relevant operation. In view of its high single pass absorption, hydrogen minority fundamental cyclotron heating in a deuterium plasma was chosen as the reference wave heating scheme in the ion cyclotron domain of frequencies. The present paper discusses the plasma behavior as a function of the minority concentration X[H] in L-mode with up to 4MW of RF power. It was found that the tungsten concentration decreases by a factor of 4 when the minority concentration is increased from X[H] ≈ 5% to X[H] % 20% and that it remains at a similar level when X[H] is further increased to 30%; a monotonic decrease in Beryllium emission is simultaneously observed. The radiated power drops by a factor of 2 and reaches a minimum at X[H] ≈ 20%. It is discussed that poor single pass absorption at too high minority concentrations ultimately tailors the avoidance of the RF induced impurity influx. The edge density being different for different minority concentrations, it is argued that the impact ICRH has on the fate of heavy ions is not only a result of core (wave and transport) physics but also of edge dynamics and fueling