Numerical electrokinetics

A new lattice method is presented in order to efficiently solve the electrokinetic equations, which describe the structure and dynamics of the charge cloud and the flow field surrounding a single charged colloidal sphere, or a fixed array of such objects. We focus on calculating the electrophoretic mobility in the limit of small driving field, and systematically linearise the equations with respect to the latter. This gives rise to several subproblems, each of which is solved by a specialised numerical algorithm. For the total problem we combine these solvers in an iterative procedure. Applying this method, we study the effect of the screening mechanism (salt screening vs. counterion screening) on the electrophoretic mobility, and find a weak non-trivial dependence, as expected from scaling theory. Furthermore, we find that the orientation of the charge cloud (i. e. its dipole moment) depends on the value of the colloid charge, as a result of a competition between electrostatic and hydrodynamic effects.Comment: accepted for publication in Journal of Physics Condensed Matter (proceedings of the 2012 CODEF conference

The role of integrated databases in microbial genome sequence analysis and metabolic reconstruction

This paper provides an overview of the PUMA system which provides access to data about metabolic pathways, enzymes, compounds, organisms, encoded activity, and assay condition information for enzymes in particular organisms and multiple sequence alignments

Outbursts of EX Hydrae: mass-transfer events or disc instabilities?

We present the 45-yr record of the light curve of EX Hya, and discuss the characteristics of its 15 observed outbursts. We then concentrate on the 1998 outburst, reporting the first outburst X-ray observations. We discover an X-ray beat-cycle modulation, indicating that an enhanced accretion stream couples directly with the magnetosphere in outburst, confirming our previous prediction. Optical eclipse profiles late in outburst show that the visible light is dominated by an enhanced mass-transfer stream overflowing the accretion disc. We are uncertain whether the enhanced mass transfer is triggered by a disc instability, or by some other cause. While in outburst, EX Hya shows some of the characteristics of SW Sex stars

Solar System Objects in the ISOPHOT 170 micron Serendipity Survey

The ISOPHOT Serendipity Survey (ISOSS) covered approximately 15 % of the sky at a wavelength of 170 micron while the ISO satellite was slewing from one target to the next. By chance ISOSS slews went over many solar system objects (SSOs). We identified the comets, asteroids and planets in the slews through a fast and effective search procedure based on N-body ephemeris and flux estimates. The detections were analysed from a calibration and scientific point of view. Through the measurements of the well-known asteroids Ceres, Pallas, Juno and Vesta and the planets Uranus and Neptune it was possible to improve the photometric calibration of ISOSS and to extend it to higher flux regimes. We were also able to establish calibration schemes for the important slew end data. For the other asteroids we derived radiometric diameters and albedos through a recent thermophysical model. The scientific results are discussed in the context of our current knowledge of size, shape and albedos, derived from IRAS observations, occultation measurements and lightcurve inversion techniques. In all cases where IRAS observations were available we confirm the derived diameters and albedos. For the five asteroids without IRAS detections only one was clearly detected and the radiometric results agreed with sizes given by occultation and HST observations. Four different comets have clearly been detected at 170 micron and two have marginal detections. The observational results are presented to be used by thermal comet models in the future. The nine ISOSS slews over Hale-Bopp revealed extended and asymmetric structures related to the dust tail. We attribute the enhanced emission in post-perihelion observations to large particles around the nucleus. The signal patterns are indicative of a concentration of the particles in trail direction.Comment: 15 pages, 6 figures, 6 tables; Accepted for publication in Astronomy and Astrophysic

Self-similarity of complex networks

Complex networks have been studied extensively due to their relevance to many real systems as diverse as the World-Wide-Web (WWW), the Internet, energy landscapes, biological and social networks \cite{ab-review,mendes,vespignani,newman,amaral}. A large number of real networks are called ``scale-free'' because they show a power-law distribution of the number of links per node \cite{ab-review,barabasi1999,faloutsos}. However, it is widely believed that complex networks are not {\it length-scale} invariant or self-similar. This conclusion originates from the ``small-world'' property of these networks, which implies that the number of nodes increases exponentially with the ``diameter'' of the network \cite{erdos,bollobas,milgram,watts}, rather than the power-law relation expected for a self-similar structure. Nevertheless, here we present a novel approach to the analysis of such networks, revealing that their structure is indeed self-similar. This result is achieved by the application of a renormalization procedure which coarse-grains the system into boxes containing nodes within a given "size". Concurrently, we identify a power-law relation between the number of boxes needed to cover the network and the size of the box defining a finite self-similar exponent. These fundamental properties, which are shown for the WWW, social, cellular and protein-protein interaction networks, help to understand the emergence of the scale-free property in complex networks. They suggest a common self-organization dynamics of diverse networks at different scales into a critical state and in turn bring together previously unrelated fields: the statistical physics of complex networks with renormalization group, fractals and critical phenomena.Comment: 28 pages, 12 figures, more informations at http://www.jamlab.or

Volume terms for charged colloids: a grand-canonical treatment

We present a study of thermodynamic properties of suspensions of charged colloids on the basis of linear Poisson-Boltzmann theory. We calculate the effective Hamiltonian of the colloids by integrating out the ionic degrees of freedom grand-canonically. This procedure not only yields the well-known pairwise screened-Coulomb interaction between the colloids, but also additional volume terms which affect the phase behavior and the thermodynamic properties such as the osmotic pressure. These calculations are greatly facilitated by the grand-canonical character of our treatment of the ions, and allow for relatively fast computations compared to earlier studies in the canonical ensemble. Moreover, the present derivation of the volume terms are relatively simple, make a direct connection with Donnan equilibrium, yield an explicit expression for the effective screening constant, and allow for extensions to include, for instance, nonlinear effects.Comment: 16 pages, 6 figures, published in Phys.Rev.

Outbursts of EX Hydrae: mass-transfer events or disc instabilities?

We present the 45-yr record of EX Hya's lightcurve and discuss the characteristics of its 15 observed outbursts. We then concentrate on the 1998 outburst, reporting the first outburst X-ray observations. We discover an X-ray beat-cycle modulation, indicating that an enhanced accretion stream couples directly with the magnetosphere in outburst, confirming our previous prediction. Optical eclipse profiles late in outburst show that the visible light is dominated by an enhanced mass-transfer stream overflowing the accretion disc. We are uncertain whether the enhanced mass transfer is triggered by a disc instability, or by some other cause. While in outburst, EX Hya shows some of the characteristics of SW Sex stars.Comment: To appear in MNRAS (8 pages; 9 figs

A Novel Bioinformatics Strategy for Function Prediction of Poorly-Characterized Protein Genes Obtained from Metagenome Analyses

As a result of remarkable progresses of DNA sequencing technology, vast quantities of genomic sequences have been decoded. Homology search for amino acid sequences, such as BLAST, has become a basic tool for assigning functions of genes/proteins when genomic sequences are decoded. Although the homology search has clearly been a powerful and irreplaceable method, the functions of only 50% or fewer of genes can be predicted when a novel genome is decoded. A prediction method independent of the homology search is urgently needed. By analyzing oligonucleotide compositions in genomic sequences, we previously developed a modified Self-Organizing Map ‘BLSOM’ that clustered genomic fragments according to phylotype with no advance knowledge of phylotype. Using BLSOM for di-, tri- and tetrapeptide compositions, we developed a system to enable separation (self-organization) of proteins by function. Analyzing oligopeptide frequencies in proteins previously classified into COGs (clusters of orthologous groups of proteins), BLSOMs could faithfully reproduce the COG classifications. This indicated that proteins, whose functions are unknown because of lack of significant sequence similarity with function-known proteins, can be related to function-known proteins based on similarity in oligopeptide composition. BLSOM was applied to predict functions of vast quantities of proteins derived from mixed genomes in environmental samples