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)
A large computer program is typically divided into many hundreds or even thousands of smaller units, whose logical connections define a network in a natural way. This network reflects the internal structure of the program, and defines the "information flow" within the program. We show that (1) due to its growth in time this network displays a scale-free(More)
All chromosomes must be completely replicated prior to cell division, a requirement that demands the activation of a sufficient number of appropriately distributed DNA replication origins. Here we investigate how the activity of multiple origins on each chromosome is coordinated to ensure successful replication. We present a stochastic model for whole(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 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)
We show that common circulatory diseases, such as stenoses and aneurysms, generate chaotic advection of blood particles. This phenomenon has major consequences on the way the biochemical particles behave. Chaotic advection leads to a peculiar filamentary particle distribution, which in turn creates a favorable environment for particle reactions.(More)
We argue that many major features in electronic transport in realistic quantum dots are not explainable by the usual semiclassical approach, due to the contributions of the quantum-mechanical tunneling of the electrons through the Kolmogorov-Arnol'd-Moser islands. We show that dynamical tunneling gives rise to a set of resonances characterized by two(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)