Role of the particle's stepping cycle in an asymmetric exclusion process: A model of mRNA translation

Messenger RNA translation is often studied by means of statistical-mechanical models based on the Asymmetric Simple Exclusion Process (ASEP), which considers hopping particles (the ribosomes) on a lattice (the polynucleotide chain). In this work we extend this class of models and consider the two fundamental steps of the ribosome's biochemical cycle following a coarse-grained perspective. In order to achieve a better understanding of the underlying biological processes and compare the theoretical predictions with experimental results, we provide a description lying between the minimal ASEP-like models and the more detailed models, which are analytically hard to treat. We use a mean-field approach to study the dynamics of particles associated with an internal stepping cycle. In this framework it is possible to characterize analytically different phases of the system (high density, low density or maximal current phase). Crucially, we show that the transitions between these different phases occur at different parameter values than the equivalent transitions in a standard ASEP, indicating the importance of including the two fundamental steps of the ribosome's biochemical cycle into the model.Comment: 9 pages, 9 figure

Ribosome recycling induces optimal translation rate at low ribosomal availability

Funding statement The authors thank BBSRC (BB/F00513/X1, BB/I020926/1 and DTG) and SULSA for funding. Acknowledgement The authors thank R. Allen, L. Ciandrini, B. Gorgoni and P. Greulich for very helpful discussions and careful reading of the manuscript.Peer reviewedPublisher PD

Control of magnetism in singlet-triplet superconducting heterostructures

We analyze the magnetization at the interface between singlet and triplet superconductors and show that its direction and dependence on the phase difference across the junction are strongly tied to the structure of the triplet order parameter as well as to the pairing interactions. We consider equal spin helical, opposite spin chiral, and mixed symmetry pairing on the triplet side and show that the magnetization vanishes at $\phi=0$ only in the first case, follows approximately a $\cos\phi$ behavior for the second, and shows higher harmonics for the last configuration. We trace the origin of the magnetization to the magnetic structure of the Andreev bound states near the interface, and provide a symmetry-based explanation of the results. Our findings can be used to control the magnetization in superconducting heterostructures and to test symmetries of spin-triplet superconductors.Comment: 5 pages, 3 figure

Plasma flows and magnetic field interplay during the formation of a pore

We studied the formation of a pore in AR NOAA 11462. We analysed data obtained with the IBIS at the DST on April 17, 2012, consisting of full Stokes measurements of the Fe I 617.3 nm lines. Furthermore, we analysed SDO/HMI observations in the continuum and vector magnetograms derived from the Fe I 617.3 nm line data taken from April 15 to 19, 2012. We estimated the magnetic field strength and vector components and the LOS and horizontal motions in the photospheric region hosting the pore formation. We discuss our results in light of other observational studies and recent advances of numerical simulations. The pore formation occurs in less than 1 hour in the leading region of the AR. The evolution of the flux patch in the leading part of the AR is faster (< 12 hour) than the evolution (20-30 hour) of the more diffuse and smaller scale flux patches in the trailing region. During the pore formation, the ratio between magnetic and dark area decreases from 5 to 2. We observe strong downflows at the forming pore boundary and diverging proper motions of plasma in the vicinity of the evolving feature that are directed towards the forming pore. The average values and trends of the various quantities estimated in the AR are in agreement with results of former observational studies of steady pores and with their modelled counterparts, as seen in recent numerical simulations of a rising-tube process. The agreement with the outcomes of the numerical studies holds for both the signatures of the flux emergence process (e.g. appearance of small-scale mixed polarity patterns and elongated granules) and the evolution of the region. The processes driving the formation of the pore are identified with the emergence of a magnetic flux concentration and the subsequent reorganization of the emerged flux, by the combined effect of velocity and magnetic field, in and around the evolving structure.Comment: Accepted for publication in Astronomy and Astrophysic

Approximate analytical description of the nonaffine response of amorphous solids

An approximation scheme for model disordered solids is proposed that leads to the fully analytical evaluation of the elastic constants under explicit account of the inhomogeneity (nonaffinity) of the atomic displacements. The theory is in quantitative agreement with simulations for central-force systems and predicts the vanishing of the shear modulus at the isostatic point with the linear law {\mu} ~ (z - 2d), where z is the coordination number. The vanishing of rigidity at the isostatic point is shown to be a consequence of the canceling out of positive affine and negative nonaffine terms

Nonclassical Light in Interferometric Measurements

It is shown that the even and odd coherent light and other nonclassical states of light like superposition of coherent states with different phases may replace the squeezed light in interferometric gravitational wave detector to increase its sensitivity. (Contribution to the Second Workshop on Harmonic Oscillator, Cocoyoc, Mexico, March 1994)Comment: 8 pages,LATEX,preprint of Naples University, INFN-NA-IV-94/30,DSF-T-94/3

The 2003 eclipse of EE Cep is coming. A review of past eclipses

EE Cep is an eclipsing binary with a period of 5.6 years. The next eclipse will occur soon, in May-June 2003, and all available past eclipses were collected and briefly analysed. EE Cep shows very large changes of the shape and the depth of minima during different eclipses, however it is possible to single out some persistent features. The analysis suggests that the eclipsing body should be a long object surrounded by an extended semi-transparent envelope. As an explanation, a model of a precessing optically thick disc, inclined to the plane of the binary orbit, is invoked. The changes of its spatial orientation, which is defined by the inclination of the disc and the tilt, induced most probably by precession of the disc spin axis with a period of about 50 years, produce strange photometric behaviour of this star. The H_alpha emission, and possibly the NaI absorptions, show significant changes during several months outside of the eclipse phase.Comment: 7 pages, 7 figures, LaTeX2e, accepted by A&

Height dependence of the penumbral fine-scale structure in the inner solar atmosphere

We studied the physical parameters of the penumbra in a large and fully-developed sunspot, one of the largest over the last two solar cycles, by using full-Stokes measurements taken at the photospheric Fe I 617.3 nm and chromospheric Ca II 854.2 nm lines with the Interferometric Bidimensional Spectrometer. Inverting measurements with the NICOLE code, we obtained the three-dimensional structure of the magnetic field in the penumbra from the bottom of the photosphere up to the middle chromosphere. We analyzed the azimuthal and vertical gradient of the magnetic field strength and inclination. Our results provide new insights on the properties of the penumbral magnetic fields in the chromosphere at atmospheric heights unexplored in previous studies. We found signatures of the small-scale spine and intra-spine structure of both the magnetic field strength and inclination at all investigated atmospheric heights. In particular, we report typical peak-to-peak variations of the field strength and inclination of $\approx 300$ G and $\approx 20^{\circ}$, respectively, in the photosphere, and of $\approx 200$ G and $\approx 10^{\circ}$ in the chromosphere. Besides, we estimated the vertical gradient of the magnetic field strength in the studied penumbra: we find a value of $\approx 0.3$ G km$^{-1}$ between the photosphere and the middle chromosphere. Interestingly, the photospheric magnetic field gradient changes sign from negative in the inner to positive in the outer penumbra.Comment: 14 page, 9 figures, accepted for Ap

Kinematics and Magnetic Properties of a Light Bridge in a Decaying Sunspot

We present the results obtained by analyzing high spatial and spectral resolution data of the solar photosphere acquired by the CRisp Imaging SpectroPolarimeter at the Swedish Solar Telescope on 6 August 2011, relevant to a large sunspot with a light bridge (LB) observed in NOAA AR 11263. These data are complemented by simultaneous Hinode Spectropolarimeter (SP) observation in the Fe I 630.15 nm and 630.25 nm lines. The continuum intensity map shows a discontinuity of the radial distribution of the penumbral filaments in correspondence with the LB, which shows a dark lane (about 0.3" wide and about 8.0" long) along its main axis. The available data were inverted with the Stokes Inversion based on Response functions (SIR) code and physical parameters maps were obtained. The line-of-sight (LOS) velocity of the plasma along the LB derived from the Doppler effect shows motions towards and away from the observer up to 0.6 km/s, which are lower in value than the LOS velocities observed in the neighbouring penumbral filaments. The noteworthy result is that we find motions toward the observer up to 0.6 km/s in the dark lane where the LB is located between two umbral cores, while the LOS velocity motion toward the observer is strongly reduced where the LB is located between an umbral core at one side and penumbral filaments on the other side. Statistically, the LOS velocities correspond to upflows/downflows andcomparing these results with Hinode/SP data, we conclude that the surrounding magnetic field configuration (whether more or less inclined) could have a role in maintaining the conditions for the process of plasma piling up along the dark lane. The results obtained from our study support and confirm outcomes of recent magnetohydro-dynamic simulations showing upflows along the main axis of a LBs