216 research outputs found
Modern Coding Sequences Are in the Periodic-to-Chaotic Transition
It seems as though biologists are extraor-dinarily fond of randomness. A popula-tion is defined as one, randomly mating, interbreeding unit, although truly ran
Multiple-length-scale elastic instability mimics parametric resonance of nonlinear oscillators
Spatially confined rigid membranes reorganize their morphology in response to
the imposed constraints. A crumpled elastic sheet presents a complex pattern of
random folds focusing the deformation energy while compressing a membrane
resting on a soft foundation creates a regular pattern of sinusoidal wrinkles
with a broad distribution of energy. Here, we study the energy distribution for
highly confined membranes and show the emergence of a new morphological
instability triggered by a period-doubling bifurcation. A periodic
self-organized focalization of the deformation energy is observed provided an
up-down symmetry breaking, induced by the intrinsic nonlinearity of the
elasticity equations, occurs. The physical model, exhibiting an analogy with
parametric resonance in nonlinear oscillator, is a new theoretical toolkit to
understand the morphology of various confined systems, such as coated materials
or living tissues, e.g., wrinkled skin, internal structure of lungs, internal
elastica of an artery, brain convolutions or formation of fingerprints.
Moreover, it opens the way to new kind of microfabrication design of
multiperiodic or chaotic (aperiodic) surface topography via self-organization.Comment: Submitted for publicatio
Feigenbaum graphs: a complex network perspective of chaos
The recently formulated theory of horizontal visibility graphs transforms
time series into graphs and allows the possibility of studying dynamical
systems through the characterization of their associated networks. This method
leads to a natural graph-theoretical description of nonlinear systems with
qualities in the spirit of symbolic dynamics. We support our claim via the case
study of the period-doubling and band-splitting attractor cascades that
characterize unimodal maps. We provide a universal analytical description of
this classic scenario in terms of the horizontal visibility graphs associated
with the dynamics within the attractors, that we call Feigenbaum graphs,
independent of map nonlinearity or other particulars. We derive exact results
for their degree distribution and related quantities, recast them in the
context of the renormalization group and find that its fixed points coincide
with those of network entropy optimization. Furthermore, we show that the
network entropy mimics the Lyapunov exponent of the map independently of its
sign, hinting at a Pesin-like relation equally valid out of chaos.Comment: Published in PLoS ONE (Sep 2011
Distinct domains in Nbs1 regulate irradiation-induced checkpoints and apoptosis
The chromosomal instability syndromes Nijmegen breakage syndrome (NBS) and ataxia telangiectasia (AT) share many overlapping phenotypes, including cancer predisposition, radiation sensitivity, cell-cycle checkpoint defects, immunodeficiency, and gonadal dysfunction. The NBS protein Nbs1 is not only a downstream target of AT mutated (ATM) kinase but also acts upstream, promoting optimal ATM activation, ATM recruitment to breaks, and ATM accessibility to substrates. By reconstituting Nbs1 knockout mice with bacterial artificial chromosomes, we have assessed the contribution of distinct regions of Nbs1 to the ATM-dependent DNA damage response. We fi nd that T cell and oocyte development, as well as DNA damage-induced G2/M and S phase checkpoint arrest and radiation survival are dependent on the N-terminal forkhead-associated domain, but not on the principal residues phosphorylated by ATM (S278 and S343) or on the evolutionarily conserved C-terminal region of Nbs1. However, the C-terminal region regulates irradiation-induced apoptosis. These studies provide insight into the complex interplay between Nbs1 and ATM in the DNA damage response
Physics Opportunities of e+e- Linear Colliders
We describe the anticipated experimental program of an e+e- linear collider
in the energy range 500 GeV -- 1.5 TeV. We begin with a description of current
collider designs and the expected experimental environment. We then discuss
precision studies of the W boson and top quark. Finally, we review the range of
models proposed to explain the physics of electroweak symmetry breaking and
show, for each case, the central role that the linear collider experiments will
play in elucidating this physics. (to appear in Annual Reviews of Nuclear and
Particle Science)Comment: 93 pages, latex + 23 figures; typos corrections + 1 reference adde
Strange Attractors in Dissipative Nambu Mechanics : Classical and Quantum Aspects
We extend the framework of Nambu-Hamiltonian Mechanics to include dissipation
in phase space. We demonstrate that it accommodates the phase space
dynamics of low dimensional dissipative systems such as the much studied Lorenz
and R\"{o}ssler Strange attractors, as well as the more recent constructions of
Chen and Leipnik-Newton. The rotational, volume preserving part of the flow
preserves in time a family of two intersecting surfaces, the so called {\em
Nambu Hamiltonians}. They foliate the entire phase space and are, in turn,
deformed in time by Dissipation which represents their irrotational part of the
flow. It is given by the gradient of a scalar function and is responsible for
the emergence of the Strange Attractors.
Based on our recent work on Quantum Nambu Mechanics, we provide an explicit
quantization of the Lorenz attractor through the introduction of
Non-commutative phase space coordinates as Hermitian matrices in
. They satisfy the commutation relations induced by one of the two
Nambu Hamiltonians, the second one generating a unique time evolution.
Dissipation is incorporated quantum mechanically in a self-consistent way
having the correct classical limit without the introduction of external degrees
of freedom. Due to its volume phase space contraction it violates the quantum
commutation relations. We demonstrate that the Heisenberg-Nambu evolution
equations for the Quantum Lorenz system give rise to an attracting ellipsoid in
the dimensional phase space.Comment: 35 pages, 4 figures, LaTe
Physics and Applications of Laser Diode Chaos
An overview of chaos in laser diodes is provided which surveys experimental
achievements in the area and explains the theory behind the phenomenon. The
fundamental physics underpinning this behaviour and also the opportunities for
harnessing laser diode chaos for potential applications are discussed. The
availability and ease of operation of laser diodes, in a wide range of
configurations, make them a convenient test-bed for exploring basic aspects of
nonlinear and chaotic dynamics. It also makes them attractive for practical
tasks, such as chaos-based secure communications and random number generation.
Avenues for future research and development of chaotic laser diodes are also
identified.Comment: Published in Nature Photonic
Identification of novel SNPs of ABCD1, ABCD2, ABCD3, and ABCD4 genes in patients with X-linked adrenoleukodystrophy (ALD) based on comprehensive resequencing and association studies with ALD phenotypes
Adrenoleukodystrophy (ALD) is an X-linked disorder affecting primarily the white matter of the central nervous system occasionally accompanied by adrenal insufficiency. Despite the discovery of the causative gene, ABCD1, no clear genotype–phenotype correlations have been established. Association studies based on single nucleotide polymorphisms (SNPs) identified by comprehensive resequencing of genes related to ABCD1 may reveal genes modifying ALD phenotypes. We analyzed 40 Japanese patients with ALD. ABCD1 and ABCD2 were analyzed using a newly developed microarray-based resequencing system. ABCD3 and ABCD4 were analyzed by direct nucleotide sequence analysis. Replication studies were conducted on an independent French ALD cohort with extreme phenotypes. All the mutations of ABCD1 were identified, and there was no correlation between the genotypes and phenotypes of ALD. SNPs identified by the comprehensive resequencing of ABCD2, ABCD3, and ABCD4 were used for association studies. There were no significant associations between these SNPs and ALD phenotypes, except for the five SNPs of ABCD4, which are in complete disequilibrium in the Japanese population. These five SNPs were significantly less frequently represented in patients with adrenomyeloneuropathy (AMN) than in controls in the Japanese population (p = 0.0468), whereas there were no significant differences in patients with childhood cerebral ALD (CCALD). The replication study employing these five SNPs on an independent French ALD cohort, however, showed no significant associations with CCALD or pure AMN. This study showed that ABCD2, ABCD3, and ABCD4 are less likely the disease-modifying genes, necessitating further studies to identify genes modifying ALD phenotypes
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