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Z. Rapti, A. Smerzi, K. Ø. Rasmussen and A. R. Bishop 1 Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and School of Mathematics, Institute for Advanced Study, Einstein Drive 1, Princeton, New Jersey 08540 2 Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New(More)
Species interactions can strongly influence the size and dynamics of epidemics in populations of focal hosts. The "dilution effect" provides a particularly interesting type of interaction from a biological standpoint. Diluters - other host species which resist infection but remove environmentally-distributed propagules of parasites (spores) - should reduce(More)
DNA instability profiles have been used recently for predicting the transcriptional start site and the location of core promoters, and to gain insight into promoter action. It was also shown that the use of these profiles can significantly improve the performance of motif finding programs. In this work we introduce a new method for computing DNA instability(More)
  • Z Rapti
  • The European physical journal. E, Soft matter
  • 2010
We investigate a DNA model that takes into account stacking interactions with neighbors up to three bases away. The model is a generalization of the well-known Peyrard-Bishop (PB) model and is motivated by studies that suggest that nearest-neighbor models for base-pair interaction in a DNA chain might not be enough to capture the mechanism and dynamics of(More)
Variation among individuals is a prerequisite of evolution by natural selection. As such, identifying the origins of variation is a fundamental goal of biology. We investigated the link between gene interactions and variation in gene expression among individuals and species using the mammalian limb as a model system. We first built interaction networks for(More)
We showed previously that anharmonic DNA dynamical features correlate with transcriptional activity in selected viral promoters, and hypothesized that areas of DNA softness may represent loci of functional significance. The nine known promoters from human adenovirus type 5 were analyzed for inherent DNA softness using the Peyrard-Bishop-Dauxois model and a(More)
We study the stability properties of periodic solutions to the Nonlinear Schrödinger (NLS) equation with a periodic potential. We exploit the symmetries of the problem, in particular the Hamiltonian structure and the U(1) symmetry. We develop a simple sufficient criterion that guarantees the existence of a modulational instability spectrum along the(More)
Despite the growing awareness that larval competition can influence adult mosquito life history traits including susceptibility to pathogens, the net effect of larval competition on human risk of exposure to mosquito-borne pathogens remains poorly understood. We examined how intraspecific larval competition affects dengue-2 virus (DENV-2) extrinsic(More)
We study the largest Lyapunov exponent of the response of a two dimensional non-Hamiltonian system driven by additive white noise. The specific system we consider is the third-order truncated normal form of the unfolding of a Hopf bifurcation. We show that in the small-noise limit the top Lyapunov exponent always approaches zero from below (and is thus(More)