Multi-site H-bridge breathers in a DNA--shaped double strand

We investigate the formation process of nonlinear vibrational modes representing broad H-bridge multi--site breathers in a DNA--shaped double strand. Within a network model of the double helix we take individual motions of the bases within the base pair plane into account. The resulting H-bridge deformations may be asymmetric with respect to the helix axis. Furthermore the covalent bonds may be deformed distinctly in the two backbone strands. Unlike other authors that add different extra terms we limit the interaction to the hydrogen bonds within each base pair and the covalent bonds along each strand. In this way we intend to make apparent the effect of the characteristic helicoidal structure of DNA. We study the energy exchange processes related with the relaxation dynamics from a non-equilibrium conformation. It is demonstrated that the twist-opening relaxation dynamics of a radially distorted double helix attains an equilibrium regime characterized by a multi-site H-bridge breather.Comment: 27 pages and 10 figure

Stationary and moving breathers in a simplified model of curved alpha--helix proteins

The existence, stability and movability of breathers in a model for alpha-helix proteins is studied. This model basically consists a chain of dipole moments parallel to it. The existence of localized linear modes brings about that the system has a characteristic frequency, which depends on the curvature of the chain. Hard breathers are stable, while soft ones experiment subharmonic instabilities that preserve, however the localization. Moving breathers can travel across the bending point for small curvature and are reflected when it is increased. No trapping of breathers takes place.Comment: 19 pages, 11 figure

Discrete breathers in dissipative lattices

We study the properties of discrete breathers, also known as intrinsic localized modes, in the one-dimensional Frenkel-Kontorova lattice of oscillators subject to damping and external force. The system is studied in the whole range of values of the coupling parameter, from C=0 (uncoupled limit) up to values close to the continuum limit (forced and damped sine-Gordon model). As this parameter is varied, the existence of different bifurcations is investigated numerically. Using Floquet spectral analysis, we give a complete characterization of the most relevant bifurcations, and we find (spatial) symmetry-breaking bifurcations which are linked to breather mobility, just as it was found in Hamiltonian systems by other authors. In this way moving breathers are shown to exist even at remarkably high levels of discreteness. We study mobile breathers and characterize them in terms of the phonon radiation they emit, which explains successfully the way in which they interact. For instance, it is possible to form ``bound states'' of moving breathers, through the interaction of their phonon tails. Over all, both stationary and moving breathers are found to be generic localized states over large values of $C$, and they are shown to be robust against low temperature fluctuations.Comment: To be published in Physical Review

Ecological genetics of freshwater fish: a short review of the genotype–phenotype connection

Genética ecológica de los peces de agua dulce: una breve revisión de la conexión genotipo–fenotipo La ecología molecular o la genética ecológica es una aplicación de la genética de poblaciones que durante las dos últimas décadas ha sufrido un proceso de expansión. Sin embargo, en la ecología molecular predominan los estudios sistemáticos y filogeográficos, con relativamente poco énfasis en el análisis de la base genética del proceso de adaptación a diferentes condiciones ecológicas. Esta relación entre genotipo y fenotipo adaptativo es poco evidente, porque las poblaciones son difíciles de cuantificar y los experimentos son logísticamente complicados. Es interesante destacar que en peces de agua dulce estos estudios no son tan poco frecuentes como en otros grupos de vertebrados. En esta revisión, nuestra intención es resumir los pocos casos en los cuales la relación entre ecología y genética de peces continentales está más desarrollada, principalmente entre marcadores genéticos y fenotipos ecológicos. Palabras clave: Genética ecológica, Ecología molecular, Interacción genotipo–fenotipo, Adaptación, Genética del paisaje, Introducción de especies.Molecular ecology or ecological genetics is an expanding application of population genetics which has flourished in the last two decades but it is dominated by systematic and phylogeographic studies, with relatively little emphasis on the study of the genetic basis of the process of adaptation to different ecological conditions. The relationship between genotype and adaptive phenotypes is weak because populations are often difficult to quantify and experiments are logistically challenging or unfeasible. Interestingly, in freshwater fish, studies to characterize the genetic architecture of adaptive traits are not as rare as in other vertebrate groups. In this review, we summarize the few cases where the relationship between the ecology and genetics of freshwater fish is more developed, namely the relationship between genetic markers and ecological phenotypes. Key words: Ecological genetics, Molecular ecology, Genotype–phenotype relationship, Adaptation, Landscape genetics, Species introduction.Genética ecológica de los peces de agua dulce: una breve revisión de la conexión genotipo–fenotipo La ecología molecular o la genética ecológica es una aplicación de la genética de poblaciones que durante las dos últimas décadas ha sufrido un proceso de expansión. Sin embargo, en la ecología molecular predominan los estudios sistemáticos y filogeográficos, con relativamente poco énfasis en el análisis de la base genética del proceso de adaptación a diferentes condiciones ecológicas. Esta relación entre genotipo y fenotipo adaptativo es poco evidente, porque las poblaciones son difíciles de cuantificar y los experimentos son logísticamente complicados. Es interesante destacar que en peces de agua dulce estos estudios no son tan poco frecuentes como en otros grupos de vertebrados. En esta revisión, nuestra intención es resumir los pocos casos en los cuales la relación entre ecología y genética de peces continentales está más desarrollada, principalmente entre marcadores genéticos y fenotipos ecológicos. Palabras clave: Genética ecológica, Ecología molecular, Interacción genotipo–fenotipo, Adaptación, Genética del paisaje, Introducción de especies

Effect of the Introduction of Impurities on the Stability Properties of Multibreathers at Low Coupling

sing a theorem dubbed the {\em Multibreather Stabiliy Theorem} [Physica D 180 (2003) 235-255] we have obtained the stability properties of multibreathers in systems of coupled oscillators with on-site potentials, with an inhomogeneity. Analytical results are obtained for 2-site, 3-site breathers, multibreathers, phonobreathers and dark breathers. The inhomogeneity is considered both at the on-site potential and at the coupling terms. All the results have been checked numerically with excellent agreement. The main conclusion is that the introduction of a impurity does not alter the stability properties.Comment: 20 pages, 9 figure

Thermal diagnostic of the Optical Window on board LISA Pathfinder

Vacuum conditions inside the LTP Gravitational Reference Sensor must comply with rather demanding requirements. The Optical Window (OW) is an interface which seals the vacuum enclosure and, at the same time, lets the laser beam go through for interferometric Metrology with the test masses. The OW is a plane-parallel plate clamped in a Titanium flange, and is considerably sensitive to thermal and stress fluctuations. It is critical for the required precision measurements, hence its temperature will be carefully monitored in flight. This paper reports on the results of a series of OW characterisation laboratory runs, intended to study its response to selected thermal signals, as well as their fit to numerical models, and the meaning of the latter. We find that a single pole ARMA transfer function provides a consistent approximation to the OW response to thermal excitations, and derive a relationship with the physical processes taking place in the OW. We also show how system noise reduction can be accomplished by means of that transfer function.Comment: 20 pages, 14 figures; accepted for publication in Class. Quantum Gra

Stability of non-time-reversible phonobreathers

Non-time reversible phonobreathers are non-linear waves that can transport energy in coupled oscillator chains by means of a phase-torsion mechanism. In this paper, the stability properties of these structures have been considered. It has been performed an analytical study for low-coupling solutions based upon the so called {\em multibreather stability theorem} previously developed by some of the authors [Physica D {\bf 180} 235]. A numerical analysis confirms the analytical predictions and gives a detailed picture of the existence and stability properties for arbitrary frequency and coupling.Comment: J. Phys. A.:Math. and Theor. In Press (2010

Patterning of the basal telencephalon and hypothalamus is essential for guidance of cortical projections

PMID: 11830575We have investigated the mechanisms that control the guidance of corticofugal projections as they extend along different subdivisions of the forebrain. To this aim, we analyzed the development of cortical projections in mice that lack Nkx2-1, a homeobox gene whose expression is restricted to two domains within the forebrain: the basal telencephalon and the hypothalamus. Molecular respecification of the basal telencephalon and hypothalamus in Nkx2-1-deficient mice causes a severe defect in the guidance of layer 5 cortical projections and ascending fibers of the cerebral peduncle. These axon tracts take an abnormal path when coursing through both the basal telencephalon and hypothalamus. By contrast, loss of Nkx2-1 function does not impair guidance of corticothalamic or thalamocortical axons. In vitro experiments demonstrate that the basal telencephalon and the hypothalamus contain an activity that repels the growth of cortical axons, suggesting that loss of this activity is the cause of the defects observed in Nkx2-1 mutants. Furthermore, analysis of the expression of candidate molecules in the basal telencephalon and hypothalamus of Nkx2-1 mutants suggests that Slit2 contributes to this activity.This work was supported by the research grants to J. L. R. R. from Nina Ireland, NARSAD, NIDA (R01DA12462) and NIMH (RO1 MH49428-01, RO1 MH51561-01A1 and K02 MH01046-01). O. M. is a NARSAD Young Investigator Award recipient and a UC Davis MIND Institute Scholar.Peer reviewe

Extracting Hα\alpha flux from photometric data in the J-PLUS survey

We present the main steps that will be taken to extract H$\alpha$ emission flux from Javalambre Photometric Local Universe Survey (J-PLUS) photometric data. For galaxies with $z\lesssim0.015$, the H$\alpha$+[NII] emission is covered by the J-PLUS narrow-band filter $F660$. We explore three different methods to extract the H$\alpha$ + [NII] flux from J-PLUS photometric data: a combination of a broad-band and a narrow-band filter ($r'$ and $F660$), two broad-band and a narrow-band one ($r'$, $i'$ and $F660$), and a SED-fitting based method using 8 photometric points. To test these methodologies, we simulated J-PLUS data from a sample of 7511 SDSS spectra with measured H$\alpha$ flux. Based on the same sample, we derive two empirical relations to correct the derived H$\alpha$+[NII] flux from dust extinction and [NII] contamination. We find that the only unbiased method is the SED fitting based one. The combination of two filters underestimates the measurements of the H$\alpha$ + [NII] flux by a 28%, while the three filters method by a 9%. We study the error budget of the SED-fitting based method and find that, in addition to the photometric error, our measurements have a systematic uncertainty of a 4.3%. Several sources contribute to this uncertainty: differences between our measurement procedure and the one used to derive the spectroscopic values, the use of simple stellar populations as templates, and the intrinsic errors of the spectra, which were not taken into account. Apart from that, the empirical corrections for dust extinction and [NII] contamination add an extra uncertainty of 14%. Given the J-PLUS photometric system, the best methodology to extract H$\alpha$ + [NII] flux is the SED-fitting based one. Using this method, we are able to recover reliable H$\alpha$ fluxes for thousands of nearby galaxies in a robust and homogeneous way.Comment: 11 pages, 14 figures. Minor changes to match the published versio