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

Reducing sample variance: halo biasing, non-linearity and stochasticity

Comparing clustering of differently biased tracers of the dark matter distribution offers the opportunity to reduce the cosmic variance error in the measurement of certain cosmological parameters. We develop a formalism that includes bias non-linearities and stochasticity. Our formalism is general enough that can be used to optimise survey design and tracers selection and optimally split (or combine) tracers to minimise the error on the cosmologically interesting quantities. Our approach generalises the one presented by McDonald & Seljak (2009) of circumventing sample variance in the measurement of $f\equiv d \ln D/d\ln a$. We analyse how the bias, the noise, the non-linearity and stochasticity affect the measurements of $Df$ and explore in which signal-to-noise regime it is significantly advantageous to split a galaxy sample in two differently-biased tracers. We use N-body simulations to find realistic values for the parameters describing the bias properties of dark matter haloes of different masses and their number density. We find that, even if dark matter haloes could be used as tracers and selected in an idealised way, for realistic haloes, the sample variance limit can be reduced only by up to a factor $\sigma_{2tr}/\sigma_{1tr}\simeq 0.6$. This would still correspond to the gain from a three times larger survey volume if the two tracers were not to be split. Before any practical application one should bear in mind that these findings apply to dark matter haloes as tracers, while realistic surveys would select galaxies: the galaxy-host halo relation is likely to introduce extra stochasticity, which may reduce the gain further.Comment: 21 pages, 13 figures. Published version in MNRA

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

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

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

Integral Field Spectroscopy based H\alpha\ sizes of local Luminous and Ultraluminous Infrared Galaxies. A Direct Comparison with high-z Massive Star Forming Galaxies

Aims. We study the analogy between local U/LIRGs and high-z massive SFGs by comparing basic H{\alpha} structural characteristics, such as size, and luminosity (and SFR) surface density, in an homogeneous way (i.e. same tracer and size definition, similar physical scales). Methods. We use Integral Field Spectroscopy based H{\alpha} emission maps for a representative sample of 54 local U/LIRGs (66 galaxies). From this initial sample we select 26 objects with H{\alpha} luminosities (L(H{\alpha})) similar to those of massive (i.e. M\ast \sim 10^10 M\odot or larger) SFGs at z \sim 2, and observed on similar physical scales. Results. The sizes of the H{\alpha} emitting region in the sample of local U/LIRGs span a large range, with r1/2(H{\alpha}) from 0.2 to 7 kpc. However, about 2/3 of local U/LIRGs with Lir > 10^11.4 L\odot have compact H{\alpha} emission (i.e. r1/2 < 2 kpc). The comparison sample of local U/LIRGs also shows a higher fraction (59%) of objects with compact H{\alpha} emission than the high-z sample (25%). This gives further support to the idea that for this luminosity range the size of the star forming region is a distinctive factor between local and distant galaxies of similar SF rates. However, when using H{\alpha} as a tracer for both local and high-z samples, the differences are smaller than the ones recently reported using a variety of other tracers. Despite of the higher fraction of galaxies with compact H{\alpha} emission, a sizable group (\sim 1/3) of local U/LIRGs are large (i.e. r1/2 > 2 kpc). These are systems showing pre-coalescence merger activity and they are indistinguishable from the massive high-z SFGs galaxies in terms of their H{\alpha} sizes, and luminosity and SFR surface densities.Comment: Accepted for publication in A&A. (!5 pages, 7 figures, 2 tables

Openness in Teachers' Digital Competence Frameworks: Looking for the Open Educator

There has been a wide variety of definitions of digital competence, from early narrow and technology-focused explanations to more recent attempts , such as the one by Ferrari (2013), who describes it as a complex concept encompassing a wide set of skills, attitudes and knowledge when performing tasks with Information and Communication Technologies (ICT). Furthermore, there have been various different attempts to describe teachers’ digital competence, as the literature review by McGarr and McDonagh (2019) demonstrates. These authors evidence that models either depict teachers’ digital competence in diverse taxonomies of areas and dimensions, or as a hierarchical and progressive evolution from low to high levels of awareness and ability. They observe that openness does not have a presence in most of the taxonomic models and thus they propose openness as a dimension of their four-part model, under the label of attitudes. In this current work, we analyse international and national teachers’ digital competence frameworks and review whether openness has been included in them, and, if so, how it is described. In the case of frameworks that offer a model of increasing performance, we observe the levels at which open-related concepts appear. An initial review of the frameworks by the European Commission, UNESCO, ISTE (US) and INTEF (Spain) indicates that ‘openness’ typically does not constitute a dimension in itself and tends to appear at intermediate and high levels of teachers’ digital competence, except from the UNESCO framework, where access to OER (Open Educational Resources) is present already at the lowest level. In this paper we reflect on the need for international and national frameworks of teacher professional development to boost openness: in particular, for open educational practices to be included at lower levels of teachers’ pre-service and in-service professional education. We argue that becoming an open educator requires both the development of the dispositions associated with reflective practice and the confidence to challenge neo-liberal educational assumptions in order to embrace participatory, equitable and open educational practices from the early stages of the development of teachers’ digital competence

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

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

Gene body DNA methylation in seagrasses: inter- and intraspecific differences and interaction with transcriptome plasticity under heat stress

The role of DNA methylation and its interaction with gene expression and transcriptome plasticity is poorly understood, and current insight comes mainly from studies in very few model plant species. Here, we study gene body DNA methylation (gbM) and gene expression patterns in ecotypes from contrasting thermal environments of two marine plants with contrasting life history strategies in order to explore the potential role epigenetic mechanisms could play in gene plasticity and responsiveness to heat stress. In silico transcriptome analysis of CpG(O/E) ratios suggested that the bulk of Posidonia oceanica and Cymodocea nodosa genes possess high levels of intragenic methylation. We also observed a correlation between gbM and gene expression flexibility: genes with low DNA methylation tend to show flexible gene expression and plasticity under changing conditions. Furthermore, the empirical determination of global DNA methylation (5-mC) showed patterns of intra and inter-specific divergence that suggests a link between methylation level and the plants' latitude of origin and life history. Although we cannot discern whether gbM regulates gene expression or vice versa, or if other molecular mechanisms play a role in facilitating transcriptome responsiveness, our findings point to the existence of a relationship between gene responsiveness and gbM patterns in marine plants