Modeling the emergence of polarity patterns for the intercellular transport of auxin in plants

The hormone auxin is actively transported throughout plants via protein machineries including the dedicated transporter known as PIN. The associated transport is ordered with nearby cells driving auxin flux in similar directions. Here we provide a model of both the auxin transport and of the dynamics of cellular polarisation based on flux sensing. Our main findings are: (i) spontaneous intracellular PIN polarisation arises if PIN recycling dynamics are sufficiently non-linear, (ii) there is no need for an auxin concentration gradient, and (iii) ordered multi-cellular patterns of PIN polarisation are favored by molecular noise.Comment: 17 pages and 9 figures (Main Text), 9 pages and 4 figures (Supplementary Material), revised version with some rearrangement

Ab initio theory of Fano resonances in plasmonic nanostructures and metamaterials

An ab initio theory for Fano resonances in plasmonic nanostructures and metamaterials is developed using Feshbach formalism. It reveals the role played by the electromagnetic modes and material losses in the system, and enables the engineering of Fano resonances in arbitrary geometries. A general formula for the asymmetric resonance in a non-conservative system is derived. The influence of the electromagnetic interactions on the resonance line shape is discussed and it is shown that intrinsic losses drive the resonance contrast, while its width is mostly determined by the coupling strength between the non-radiative mode and the continuum. The analytical model is in perfect agreement with numerical simulations.Comment: 13 pages, 5 figure

Constrained Allocation Flux Balance Analysis

New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism, combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis. We introduce here Constrained Allocation Flux Balance Analysis, CAFBA, in which the biosynthetic costs associated to growth are accounted for in an effective way through a single additional genome-wide constraint. Its roots lie in the experimentally observed pattern of proteome allocation for metabolic functions, allowing to bridge regulation and metabolism in a transparent way under the principle of growth-rate maximization. We provide a simple method to solve CAFBA efficiently and propose an "ensemble averaging" procedure to account for unknown protein costs. Applying this approach to modeling E. coli metabolism, we find that, as the growth rate increases, CAFBA solutions cross over from respiratory, growth-yield maximizing states (preferred at slow growth) to fermentative states with carbon overflow (preferred at fast growth). In addition, CAFBA allows for quantitatively accurate predictions on the rate of acetate excretion and growth yield based on only 3 parameters determined by empirical growth laws.Comment: 21 pages, 6 figures (main) + 33 pages, various figures and tables (supporting); for the supplementary MatLab code, see http://tinyurl.com/h763es

Challenges in experimental data integration within genome-scale metabolic models

A report of the meeting "Challenges in experimental data integration within genome-scale metabolic models", Institut Henri Poincar\'e, Paris, October 10-11 2009, organized by the CNRS-MPG joint program in Systems Biology.Comment: 5 page

Magnetic exponents of two-dimensional spin glasses

The magnetic critical properties of two-dimensional spin glasses are controversial.Using exact ground state determination, we extract the properties of clusters flipped when increasing continuously a uniform field. We show that these clusters have many holes but otherwise have statistical properties similar to those of zero-field droplets. A detailed analysis gives for the magnetization exponent delta approx 1.30 pm 0.02 using lattice sizes up to 80 imes 80 ; this is compatible with the droplet model prediction delta = 1.282 . The reason for previous disagreements stems from the need to analyze both singular and analytic contributions in the low field regime

CODA (crossover distribution analyzer): quantitative characterization of crossover position patterns along chromosomes

<p>Abstract</p> <p>Background</p> <p>During meiosis, homologous chromosomes exchange segments via the formation of crossovers. This phenomenon is highly regulated; in particular, crossovers are distributed heterogeneously along the physical map and rarely arise in close proximity, a property referred to as "interference". Crossover positions form patterns that give clues about how crossovers are formed. In several organisms including yeast, tomato, <it>Arabidopsis</it>, and mouse, it is believed that crossovers form via at least two pathways, one interfering, the other not.</p> <p>Results</p> <p>We have developed a software package - "CODA", for CrossOver Distribution Analyzer - which allows one to quantitatively characterize crossover patterns by fitting interference models to experimental data. Two families of interfering models are provided: the "gamma" model and the "beam-film" model. The user can specify single or two-pathways modeling, and the software package infers the model's parameters and their confidence intervals. CODA can handle data produced from measurements on bivalents or gametes, in the form of continuous crossover positions or marker genotyping. We illustrate the possibilities on data from Wheat, corn and mouse.</p> <p>Conclusions</p> <p>CODA extends the kind of crossover data that could be analyzed so far to include gametic data (rather than only bivalents/tetrads) when using two-pathways modeling. It will also enable users to perform analyses based on the beam-film model. CODA implements that model's complex physics and mathematics, and uses a summary statistic to overcomes the lack of a computable likelihood which has hampered its use till now.</p