Alessandro P. S. de Moura

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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)
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)
The topological structure of basin boundaries plays a fundamental role in the sensitivity to the final state in chaotic dynamical systems. Herewith we present a study on the dynamics of dissipative systems close to the Hamiltonian limit, emphasizing the increasing number of periodic attractors, and on the structural changes in their basin boundaries as the(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)
The major fungal pathogen of humans, Candida albicans, mounts robust responses to oxidative stress that are critical for its virulence. These responses counteract the reactive oxygen species (ROS) that are generated by host immune cells in an attempt to kill the invading fungus. Knowledge of the dynamical processes that instigate C. albicans oxidative(More)
Methylglyoxal (MG) elicits activation of K(+) efflux systems to protect cells against the toxicity of the electrophile. ChIP-chip targeting RNA polymerase, supported by a range of other biochemical measurements and mutant creation, was used to identify genes transcribed in response to MG and which complement this rapid response. The SOS DNA repair regulon(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)
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)