Newton's method and Baker domains

We show that there exists an entire function f without zeros for which the associated Newton function N(z)=z-f(z)/f'(z) is a transcendental meromorphic functions without Baker domains. We also show that there exists an entire function f with exactly one zero for which the complement of the immediate attracting basin has at least two components and contains no invariant Baker domains of N. The second result answers a question of J. Rueckert and D. Schleicher while the first one gives a partial answer to a question of X. Buff.Comment: 6 page

Singular measures in circle dynamics

Critical circle homeomorphisms have an invariant measure totally singular with respect to the Lebesgue measure. We prove that singularities of the invariant measure are of Holder type. The Hausdorff dimension of the invariant measure is less than 1 but greater than 0

Renormalisation-induced phase transitions for unimodal maps

The thermodynamical formalism is studied for renormalisable maps of the interval and the natural potential $-t \log|Df|$. Multiple and indeed infinitely many phase transitions at positive $t$ can occur for some quadratic maps. All unimodal quadratic maps with positive topological entropy exhibit a phase transition in the negative spectrum.Comment: 14 pages, 2 figures. Revised following comments of referees. First page is blan

The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis

<p>Abstract</p> <p>Background</p> <p>Cellular response to external stimuli requires propagation of corresponding signals through molecular signaling pathways. However, signaling pathways are not isolated information highways, but rather interact in a number of ways forming sophisticated signaling networks. Since defects in signaling pathways are associated with many serious diseases, understanding of the crosstalk between them is fundamental for designing molecularly targeted therapy. Unfortunately, we still lack technology that would allow high throughput detailed measurement of activity of individual signaling molecules and their interactions. This necessitates developing methods to prioritize selection of the molecules such that measuring their activity would be most informative for understanding the crosstalk. Furthermore, absence of the reaction coefficients necessary for detailed modeling of signal propagation raises the question whether simple parameter-free models could provide useful information about such pathways.</p> <p>Results</p> <p>We study the combined signaling network of three major pro-survival signaling pathways: <b>E</b>pidermal <b>G</b>rowth <b>F</b>actor <b>R</b>eceptor (EGFR), <b>I</b>nsulin-like <b>G</b>rowth <b>F</b>actor-1 <b>R</b>eceptor (IGF-1R), and <b>I</b>nsulin <b>R</b>eceptor (IR). Our study involves static analysis and dynamic modeling of this network, as well as an experimental verification of the model by measuring the response of selected signaling molecules to differential stimulation of EGF, IGF and insulin receptors. We introduced two novel measures of the importance of a node in the context of such crosstalk. Based on these measures several molecules, namely Erk1/2, Akt1, Jnk, p70S6K, were selected for monitoring in the network simulation and for experimental studies. Our simulation method relies on the Boolean network model combined with stochastic propagation of the signal. Most (although not all) trends suggested by the simulations have been confirmed by experiments.</p> <p>Conclusion</p> <p>The simple model implemented in this paper provides a valuable first step in modeling signaling networks. However, to obtain a fully predictive model, a more detailed knowledge regarding parameters of individual interactions might be necessary.</p

Complex maps without invariant densities

We consider complex polynomials $f(z) = z^\ell+c_1$ for $\ell \in 2\N$ and $c_1 \in \R$, and find some combinatorial types and values of $\ell$ such that there is no invariant probability measure equivalent to conformal measure on the Julia set. This holds for particular Fibonacci-like and Feigenbaum combinatorial types when $\ell$ sufficiently large and also for a class of `long-branched' maps of any critical order.Comment: Typos corrected, minor changes, principally to Section

Topological entropy and secondary folding

A convenient measure of a map or flow's chaotic action is the topological entropy. In many cases, the entropy has a homological origin: it is forced by the topology of the space. For example, in simple toral maps, the topological entropy is exactly equal to the growth induced by the map on the fundamental group of the torus. However, in many situations the numerically-computed topological entropy is greater than the bound implied by this action. We associate this gap between the bound and the true entropy with 'secondary folding': material lines undergo folding which is not homologically forced. We examine this phenomenon both for physical rod-stirring devices and toral linked twist maps, and show rigorously that for the latter secondary folds occur.Comment: 13 pages, 8 figures. pdfLaTeX with RevTeX4 macro

SimBoolNet—a Cytoscape plugin for dynamic simulation of signaling networks

Summary: SimBoolNet is an open source Cytoscape plugin that simulates the dynamics of signaling transduction using Boolean networks. Given a user-specified level of stimulation to signal receptors, SimBoolNet simulates the response of downstream molecules and visualizes with animation and records the dynamic changes of the network. It can be used to generate hypotheses and facilitate experimental studies about causal relations and crosstalk among cellular signaling pathways