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We define two words in a language to be connected if they express similar concepts. The network of connections among the many thousands of words that make up a language is important not only for the study of the structure and evolution of languages, but also for cognitive science. We study this issue quantitatively, by mapping out the conceptual network of(More)
Pathogenic microbes exist in dynamic niches and have evolved robust adaptive responses to promote survival in their hosts. The major fungal pathogens of humans, Candida albicans and Candida glabrata, are exposed to a range of environmental stresses in their hosts including osmotic, oxidative and nitrosative stresses. Significant efforts have been devoted to(More)
DNA damage is a hazard all cells must face, and evolution has created a number of mechanisms to repair damaged bases in the chromosome. Paradoxically, many of these repair mechanisms can create double-strand breaks in the DNA molecule which are fatal to the cell. This indicates that the connection between DNA repair and death is far from straightforward,(More)
DNA replication is an essential process in biology and its timing must be robust so that cells can divide properly. Random fluctuations in the formation of replication starting points, called origins, and the subsequent activation of proteins lead to variations in the replication time. We analyze these stochastic properties of DNA and derive the positions(More)
We propose a scheme to induce chaos in nonlinear oscillators that either are by themselves incapable of exhibiting chaos or are far away from parameter regions of chaotic behaviors. Our idea is to make use of small, judiciously chosen perturbations in the form of weak periodic signals with time-varying frequency and phase, and to drive the system into a(More)
An adequate characterization of the dynamics of Hamiltonian systems at physically relevant scales has been largely lacking. Here we investigate this fundamental problem and we show that the finite-scale Hamiltonian dynamics is governed by effective dynamical invariants, which are significantly different from the dynamical invariants that describe the(More)
In this paper we argue that the effects of irregular chaotic motion of particles transported by blood can play a major role in the development of serious circulatory diseases. Vessel wall irregularities modify the flow field, changing in a nontrivial way the transport and activation of biochemically active particles. We argue that blood particle transport(More)
We show that bifurcations in chaotic scattering manifest themselves through the appearance of an infinitely fine-scale structure of singularities in the cross section. These "rainbow singularities" are created in a cascade, which is closely related to the bifurcation cascade undergone by the set of trapped orbits (the chaotic saddle). This cascade provides(More)
We study the effects of finite-sizeness on small, neutrally buoyant, spherical particles advected by open chaotic flows. We show that, when observed in the configuration or physical space, the advected finite-size particles disperse about the unstable manifold of the chaotic saddle that governs the passive advection. Using a discrete-time system for the(More)
Saccharomyces cerevisiae senses hyperosmotic conditions via the HOG signaling network that activates the stress-activated protein kinase, Hog1, and modulates metabolic fluxes and gene expression to generate appropriate adaptive responses. The integral control mechanism by which Hog1 modulates glycerol production remains uncharacterized. An additional(More)